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# Ab Initio Calculations - Science topic

Explore the latest questions and answers in Ab Initio Calculations, and find Ab Initio Calculations experts.

Questions related to Ab Initio Calculations

When I have taken the cif file of "Sodium Vanadium Phosphate" for Na3 V2 ( P O4 )3, and when I read the poscar file in vesta or Medea VASP, it shows Na 24 atoms instead of Na 18 atoms [that is Na4V2(PO4)3]. Also the partial occupancies of Na atom is 0.805 and 0.731 which vasp cannot handle. Do we need to make a supercell or can we directly change the occupancy to 1 for Na atoms in the poscar file.

I have also attached the POSCAR file for Na3 V2 ( P O4 )3

Hello colleagues! I found that my structure is not stable at the ground state, id. 0 Kelvin ( the crystal structure change before and after relaxation, but the energy is still negative) Thus I want to perform a relaxation at a different temperature. I have found some examples on the internet, but not a relaxation one.

This is my INCAR file, any orientation will be deeply appreciated.

ISTART = 0

ICHARG = 2

NSW = 1000

IBRION = 0

ISIF = 2

POTIM = 5

TEBEG =1200

TEEND =1200

ISYM = 0

SMASS= 0

LREAL = .FALSE.

MDALGO = 2

# precision parameters

PREC = Normal

EDIFF = 1E-6

# electronic relaxation

ALGO = FAST

ENCUT = 300

ISMEAR = 0

# output options

LWAVE = .FALSE. # write or don't write WAVECAR

LCHARG = .FALSE. # write or don't write CHG and CHGCAR

Hello dear colleagues!

I am interested to know how to put atoms at the interstitial position of the cubic bcc structure, Does anybody have or know a python or package or script which can generate all the possible configurations?

e.g. In bcc, tetrahedral sites are at (0.5 0.25 0), however, in bcc there are many tetrahedral sites. Thanks

Suppose in our orginal structure we did substitutional doping. But after substitutional doping the atomic positions slightly changed . While trying to do CDD analysis in vesta it is showing warning that lattice parameters have changed. So for doing CDD should we do only single point scf calculation without optimizing atomic positions. But if we dont do ionic relaxation then the forces between the atoms is not zero and it is not true structure. So what shall we do in this case.

Thank you in Advance

Hello dear researchers.

I would like to know how to determine the number of bands of a compound ????

Thanks in advance.

For making computational chemistry calculation more faster I need a could computing platform so I created an account in AWS but I don't know how to run the guassian input file on AWS ... anyone can please kindly guide me.

Hello dear researchers

I am a new user of Abinit softwarre and want to learn it. How can I learn it, are there any tutorials or documents I can use and read?

I am using orca for ab initio calculation. Now I want to do redundant coordinate scan for various coordinates like bonds, angles, dihedrals, improper, etc. Which tools are available for that purpose which has free source code? I know about gaussian view and webMo, but both are not free.

I would like to investigate the electronic charge distribution of it, so interpreting more properties, what simulation techniques you suggest.

For the same structure, the absolute energy obtained by "qe" and "vasp" differs greatly, it seems that they have different definitions of energy, does anyone know the difference?

Can someone provide or give me an example how the VASP WAVEDER file looks like?

I want to study the interdiffusion of Ni/Ti bilayer at 500 degrees. I have relaxed the interface and calculated the interfacial energy. My next step is to do MD simulation. Should I need to convert my Ni/Ti crystal bilayer to amorphous Ni/Ti bilayer (by heating at quenching) and then use a thermodynamic ensemble to study the interfacial reaction and diffusion?

I have calculated dielectric function by the vasp by setting LOPTICS = .T. in INCAR file.I also have open the vasp.xml file, I got the following graph. But I can export the date by Graph. Anyone has any suggestion?

Dear experts,

How does one choose the bias factor in well-tempered metadynamics? From what i have read in literature, T+ΔT should be of the order of barrier height, but again how do we know the barrier before computing it? Does it mean u first perform a standard metadynamics to get an estimate of the barrier and then set up a well-tempered metadynamics? How does it even affect the FES? choosing high bias-factor vs low bias-factor? Will it change the barriers in FES? I look forward to some insights on this.

Best,

Raghav

I am trying to optimize a molecular crystal using CRYSTAL17 software. I am getting error that the basis set I am using is linearly dependent. How can I solve such issue.

I tried changing my basis set but get same error. I tried changing k points and DFT integration grid but get same error.

Please help me solve this issue or tell me what I should do to avoid this in future.

i want to calculate the phonon spectral with Negative/Imaginary frequencies signifying instabilities

Dear expert users of the SPRKKR package,

Can someone give me guidelines to resolve convergence issues in the SCF run? For pure compound, the SCF cycle gets converged quickly (within 50 electronic iterations), but with substitutional doping (~ 2%), all the maximum allowed iteration (300) gets exhausted, and the system doesn't converge. The details of the input file and error message are as follows:

**Input**

MODE SP-SREL

LLOYD

TAU BZINT= POINTS NKTAB= 250

ENERGY GRID={5} NE={30}

ImE=0.0 Ry EMIN=-0.2 Ry

SCF NITER=300 MIX=0.101 VXC=PBE

TOL=0.00001 MIXOP=0.20 ISTBRY=1

QIONSCL=0.80

NOSSITER

**Error**

*******************************************************************************

no problems with CPA-cycle !

*******************************************************************************

*******************************************************************************

300 ERR 0.113E+01 0.698E-01 EF 0.78274 -0.00105 D 83.132 M 3.0776 0.0000

ETOT -10814.43503634 SCF - cycle not converged - NSCFITER exhausted

*******************************************************************************

I used CPMD (with PBC) to perform MD with constraints at different values of a reaction coordinate, and the resulting free-energy profile, obtained after thermodynamical integration, does not appear smooth. The barrier seems OK but the product region, at large values of the reaction coordinate, exhibits oscillations. What could cause such artifacts?

hello, I'm new to VASP and I'm trying to do surface calculations but I can not extract bulk energy from my outputs. if anyone knows I'd much appreciate your help

thanks

I am calculating the band structure of S doped Strontium Titanate using vasp. After relaxing the system (using ISIF=3), the structure gets heavily changed, and Klabels and Kpath become different from the cubic pure supercell. but I have noticed in some papers that they are showing the same Klabels in both doped and undoped structures. What could be the possible reasons for different Klabels in my case?

Where the dim.exxxxx presented this as it content:

"cp: cannot stat 'DIMCAR' : No such file or directory - VASP"

Hello Everyone,

All of us who dealing with DFT also sometimes do the spin-orbit coupling calculations. Yeah if talking in terms of code than its easy to understand but what is going behind the codes to include SOC term which is relativistic in semi-classical Density functional theory.

What are the modification in the Hamiltonian part for this.

If someone has notes then please share.

Regards,

Abhinav Nag

Hello Everyone,

As we know the Density functional theory deals at a 0 kelvin temperature and using the output of DFT scf calculations we can use the Boltztrap code to give us the thermoelectric properties at finite temperature.

So which factor is mainly responsible for that temperature part coming into play while calculating thermoelectric properties.

Is it only because of the temperature dependence of the Fermi distribution function in Boltzman equations?

Hi all

I am currently working on ab-initio calculation for ceramic materials(AlN, Al2O3...) and I want to see some experimental result about band gap and fermi level pinning in order to verify my calculation data. I tried to use UPS analysis but it is hard to analyze wide band gap materials.

So is there any other recommended techniques for measuring fermi level pinning and band structure?

I am trying to run a geometry optimisation and frequency calculation using Gaussian and I get the following error:

Problem with coordinate system.

Error termination via Lnk1e in /opt/gaussian03/g03/l103.exe at Wed Feb 5 16:49:25 2014.

Does anyone have an idea of what this means and how to solve it?

My input file can be found as an attachment.

Dear Researchers:

I have attempted (QST2) calculation several times. When I try to run the input file using the workstation; the job doesn't work. However, when I try to run the same input file on a laptop, it is done without error.

I believe this is a technical issue. What would bring about this issue and How could I solve it?

I appreciate your help.

The input is:

%nprocshared=4

%mem=100MW

#p opt= (calcfc, qst2) freq b3lyp/cc-pvdz

The error is:

Old curvilinear step not converged, using linear step:

SCX= 5.06D+01 DXMaxT= 2.00-315 SCLim= 1.00-315 Fact= 1.98-317

RedCar/ORedCr failed for GTrans.

Error termination via Lnk1e in C:\G09W\l101.exe at Tue Sep 07 07:59:04 2021

Hello Everyone,

Iam trying to do the spin polarisation calculation using quantum espresso.

I tested BCC - Fe and it works by adding

nspin=2, starting_magnetisation=0.5

But for the material under research which contains four atoms it giving the total_magnetization =0 in the output file .

I did the same calculation with ELK code and the final value there is about 3.5 Bohr magneton.

I tried to reproduce the same with espresso by giving a starting magnetisation to each atoms but still it doesn't work with Quantum espresso.

Any tips that what we should keep in mind while doing such calculations. Like choice of pseudopotential, recommended values of parameters.

Thanks,

Abhinav Nag

I have been calculating the band structure of GaAs by using VASP. I have tried to plot contribution of s, p and d orbitals into electronic band structure by using p4vasp, but I want to know how to extract the data corresponding to orbitals and plot using other plotting software like gnuplot, exmgrace or origin. If any one know script file or other software which can be use then please suggest me.

I seem to be consistently producing link 9999 errors during a TS search of a structure I generated from a mod-redundant scan geometry. As an example, I scan geometry modifying the bond length (fundamentally the position of the hydrogen) of hydrogen coming off a protonated water molecule (first frame) and finally bonding to oxygen of a carbon based molecule (e.g. enolization of the carbonyl group in glucose). I take the scan geometry of where the hydrogen is halfway between both molecules, and there is a slight adjustment of the O=C double bond (as this will change to a single bond upon associating with hydr0gen HO-C). Note: During the scan geometry, there are no major changes to the over all structure e.g., big steric clashes causing a large dihedral rotation of part of the glucose.

I have then tried a couple of basis sets.

# opt=(calcfc,ts) wb97xd/3-21+g* scrf=(solvent=water)

# opt=(calcfc,ts) wb97xd/6-31+g(d,p) scrf=(solvent=water)

With the smaller basis set I was hoping to approximate a TS structure and use it as a starting structure for a larger basis set. But in either case I produce the error:

Error termination request processed by link 9999.

Error termination via Lnk1e in /usr/local/g09/l9999.exe at Wed May 21 19:31:46 2014.

With the last optimisation step looking like this:

Item Value Threshold Converged?

Maximum Force 0.086348 0.000450 NO

RMS Force 0.014307 0.000300 NO

Maximum Displacement 0.874616 0.001800 NO

RMS Displacement 0.240702 0.001200 NO

Predicted change in Energy=-1.075204D-02

Optimization stopped.

-- Wrong number of Negative eigenvalues: Desired= 1 Actual= 4

-- Flag reset to prevent archiving.

Any ideas what I can do to rectify this problem. It is becoming a bit of a habit of Gaussian to kick out these errors every time I try a TS using a frame from mod red scan bond length.

I have now turned to QST3 using the first, last and intermediate scan step to determine my TS.

Hello.

I discover VASP and I try to obtain the band structure and the density of state of a Si crystal with VASP. The final result I get is the following figure. I don't understand why my band structure has this stepped aspect. How do you think it can be explained?

Thank you in advance for your answers.

I am trying to model off-stoichiometric intermetallics which are locally dis-ordered. How to create supercells for the same in order to understand their properties? It would require large supercells to mimic adequately the real material system and will be almost impossible to do an ab-initio calculation on it. SQS is a good option and many people are using it. But I don't have any clue how to use it? Can anybody help me out there?

Regards

Subha Sanket Panda

IIT Kanpur

For doping of Zr in NiTi, the main phase is the NiTi stoichiometric phase (austenite and martensite). So I do doping of Zr in NiTi and calculate formation energy. But along with it different disordered intermetallics of NiTi are formed during experimental process like NiTi2, and Ni3Ti. So, while doing DFT calculation, should I also compare formation energies of these intermetallics with doping percentage of Zr.

I am following tutorial of Multiwfn (Multiwfn (sobereva.com)). In its tutorial () on page 516 there is a plot of DOS (image and corresponding discussion attached). In the plot green line shows OPDOS plot their is a peak corresponding to -0.8 a.u. The tutorial says that it corresponding to molecular orbit 14 (MO14). however it is not explain why this peak correspond to MO14. please let me know any explanation about it.

Suppose, I want to do doping of 6.25 at% Cu in NiTi. For that I make a 3*2*2 supercell of NiTi. the total number of atoms is 48. There I replace 3 atoms of Ni with 3 atoms of Cu. Is there any rule that the distance between the Cu atoms should be maximum so that defects dont interact among itself. Because there can be many possible combinations for Cu replacing Ni according to symmetry and neighbouring distances.

My question is about the accuracy of DFT based methods in characterising hydrogen bonding. Whether accuracy increases as we go up the Jacob's ladder of DFT functionals?

Hello friends,

So, I have a photoeletron spectra from a sillicon carbide wafer, diving into the literature I noticed that the peaks are not very reliable it is possible to have from Si+ to Si4+ oxidation sates has four possible silicon carbide oxides ? I was searching for a way to simulate these phenomena without any experience in this kind of simulation, found that ab-initio calculations are the way, being the software Gaussian 9 the most used .So I would like to know if you could advise DFT resources to learn as free software to simulate core levels. How could I estimates the shifts beetween the oxycarbides and Si Oxides ?

Best Regards

I am a new user to crystal 17 (https://www.crystal.unito.it/index.php). I was trying to optimize a molecule using crystal17 but it is throwing following error:

"ERROR **** INPUT3 **** n-D SYSTEM - SHRINKING NOT DEFINED"

which i think means I have not defined the k -mash via SHRINK keyword.

But in input I have given following keyword

**SHRINK**

**8 16**

What is the reason for this error and how to rectify it.

Hi everyone

I'm planning to do a potential energy surface scan over a specific bond for a doubly ionized Methyl Chloride (CH3Cl2+ over C-Cl bond) using Gaussian 16 (UNIX-based operating system), my question is, how to extract the energy at each point from the output file and how to specify the bond that we want to do the scan over, in the code,

the code I initially used is shown here: (I feel there should be a line specifying the CCl bond)

%chk=CCl.chk

%mem=9GB

%NProcShared=4

#scan td=(nstates=6) wb97xd/aug-cc-pvtz

CH3Cl neutral GS syn

2 1

C

H 1 B1

H 1 B2 2 A1

H 1 B3 3 A2 2 0.0

Cl 1 B4 4 A3 3 0.0

B1=1.07011

B2=1.19035

B3=1.19148

B4=1.72691

A1=94.56838

A2=69.00098

A3=52.79175

I am new to the solid state ab-initio calculations. I need to optimize the unit cell of paracetamol. For this, I required Fractional coordinates for the system. When I extract fractional coordinates from cif (attached), my calculation program always told me that my unit cell is not neutral. However, paracetamol is a neutral system so its unit cell should not be charged.

My question is how to extract Fractional coordinates in such a way that I could get a neutral unit cell of paracetamol?

My question is why I am getting a charged cell at all even if the cif file is neutral. however, when I make input file using cif file of paracetamol (image and source file attached), it always gives me charged unit cell. I can optimize charged cell but my software (https://www.crystal.unito.it/index.php) refuse to calculate the IR and RAMAN spectra for charged system.

My question is why I am getting a charged cell at all even if the cif file is neutral.

Hi all,

Is there any software or webserver to read the molecular dynamics (MD) simulation trajectory which obtained from Ab initio MD simulation to calculate the atom-atom radial distribution function (RDF).

Thanks in advance.

I am doing calculation on a bulk periodic system using VASP, but do not know what is the reference of those absolute values for conduction band minimum and valence band maximum.

A cif file represents a unit cell with minimum energy. My question is, in the start of any ab initio calculation for unit cell generated from the cif file, why we are advised to optimize cell parameters and atomic coordinates both. Can't we just optimize atomic coordinates or perform single point calculation?

For a little background, I'm interested in dabbling more into computational chemistry since I had it as a course last year for my MSc. We used Quantum Espresso back then and that's what I plan to use. My intention is just for some light DFT calculations in general for surface catalysis or with nanotubes, mostly periodic based. Planning to build a system and was wondering if the processor and RAM are enough for my purposes, which will be an 8 core Ryzen 7 3700X and 32GB, respectively. Are these enough for light to medium intensity calculations in terms of time taken for calculations to run?

I am using crystal 17 for my solid state

*ab initio*calculations. For some reason the program is not able to produce the Raman spectra but have generated born charges.Is there any way to produce Raman spectra from born charges? any suggestion will be very helpful.

Thank you

I'm not working on biomolecules, I work on Organic, Organometallic, and sometimes inorganic structures.

Do you know a simple way to apply the right calculation method? Is there any article or book that has explained how to choose the right method and basis set based on the result we seek or simply based on the structure of the compound?

thank you...

Hello Everyone,

Using quantum Espresso I have successfully did the calculations for phonon Dispersion and Phonon density of states but to understand the contribution of the elements Need to study the Projected Phonon Density of state.

If someone know the technique then please explain.

Thanks,

Abhinav Nag

I want to calculate terahertz spectra for my system but I am confuse about how to do it. The program I am using (crystal17) has two options, one is to perform frequency calculations at gamma point and calculate IR spectra which by default comes from 0 to 4000 cm

^{-1 }. Another option is to do phonon dispersion calculations (http://tutorials.crystalsolutions.eu/tutorial.html?td=dispersion&tf=dispersion-ht) which generate supercell and perform calculations on it. I am confused about if the treahartz spectra will be the regular IR spectra taken between 0 to 100 cm^{-1}or it should be calculated from the phonon dispersion calculations.Hello Everyone,

Recently I am doing some

**Phonon**branchesbased studies. For some materials the gap between the**optical and acoustic branch**is small, for some it's large and for some there is no gap.So how this gap affects the material property or what is its physical significance?

Thanks,

Abhinav Nag

I am trying to use the FMO (Fragment Molecular Orbital) method which works to make large (thousands of atoms) molecules more palatable for ab initio computational quantum-chemical calculations on a PC. There's a really good GUI to help make the fragment input (for GAMESS in my case), called Facio (see link below to website). I have a Mac and have been trying to get Facio to work on it for a while. It was originally made for Windows but there is also a Mac version available to download on the website. The website seems to last have been updated for the OS Sierra but I have OS Catalina. Is there a way to make Facio (GUI for FMO) work on Mac OS Catalina? Thanks in advance for your help.

Recently, it has been seen in many article, dealing with ab-initio calculation, that energy of formation for a compound AxBy is expressed as below -

DelE (in eV) = E(AxBy) - xE(A) - yE(B)

Where, E(AxBy) is the energy of formation of the compound and E(A) and E(B) is energy of A and B in their respective stable state. At the outset it looks perfect, but problem starts if someone use a supercell (SC) with AnxBny where n is the multiplicity of the unit cell in the SC. In such cases the energy calculated from the above equation will be multiplied by n!!

Since, the energy/mol must be a constant value for a given compound and to compare energy of formation among different compounds the above equation should be modified as -

DelE (per mol) = c/(nx+ny) [E(AnxBny) - nxE(A) -nyE(B)]

where, c is the conversion factor from eV/atom to kJ/mol

I am new to material simulation and I am willing to learn the theoretical aspects like what is k point mesh, how to interpret band diagram, how born charge results in IR spectra etc. I have experience of using DFT using gaussian 16 (modeling of reaction machnism) but don't have any experience in material simulation.

Thank you in advance.

Is there any way to find out parity from the band structure of First principle calculation ?

Any kind of help will be appreciate.

Thanks

I know we can edit the layers (and make different cifs) and do the calculation for each layer separately to find their HOMO-LUMO. But I was wondering if there's a way to calculate HOMO-LUMO of each layer, while the layers are stacked in the heterostructure in a single cif. Thanks!

*I'm using Quantum Espresso. But I guess the problem is same the regardless of the code one is using.

Popular and widely used hybrid functionals ( B3LYP, M062X, WB97XD, LC-WPBE) fail to accurately predict vertical absorption and emission (Absorption and Fluorescence) wavelengths. Recently proposed approach of tuning in range separated hybrid functionals (Long range corrected hybrid functionals) all though improves the accuracy it does not accurately predict vertical emissions (unlike vertical absorptions).

We propose a novel Excited state tuning approach in the framework of tuning range separated hybrid functionals in DFT to predict accurate vertical emissions in the article titled,

Accurate Prediction of Vertical Emission from Excited-State Tuning of Range-Separated Density Functional Theory

How can we predict accurate Fluorescence wavelengths employing DFT? Which is the most accurate DFT methodology currently available which can predict accurate Fluorescence wavelengths (Vertical emissions) ? What are the drawbacks of popular DFT Functionals like B3LYP, M062X, WB97XD, LC-WPBE etc in predicting accurate Fluorescence wavelengths (Vertical emissions) ?

Will Tuning Range separated hybrid functionals improve the accuracy ? How can we further improve the accuracy of tuning range separated hybrid functionals?

We propose a novel Excited-State Tuning approach in Range separated Hybrid functionals in DFT framework which predicts most accurate Fluorescence wavelengths (Vertical emissions).

Should we first relax the structure (Volume, cell shape and ions) with non magnetic ground state and then use ISPIN=2 for single point geometry calculation with the relaxed structure? Would this method give more stable ground state energy?

I'm working with a quaternary system, and when I try to do the variational cell relaxation (

*vc-relax*) with nonzero starting_magnetization terms added in the input file, it looks like the total energy is oscillating between two minima after 23 hours (please see attached). But when I did the same*vc-relax*without any starting_magnetization terms, it converged just fine with a total final energy (minimum).Also, as you can see in output file that the total magnetization here is zero, which shouldn't be the case since the experimental result for this cif shows otherwise with a relatively high magnetization. So any help on this would be much appreciated! Thanks in advance!

Note: I applied

*noncolin = .true.*without any*angle*terms. Previously, I also tried with*nspin = 2*(for default z-axis mag), and got the same zero magnetic moment for this material.**Following are the measure I've already taken in an effort to troubleshoot the situation without any success**: I decreased the the

*mixing_beta*to

*0.1d0*, increased

*electron_maxstep*to

*1000*(since it stops after 100 iterations by default if the solution doesn't converge). And I only added nonzero starting_magnetization for para and ferro magnetic elements (and excluded dia/non magnetic atoms). I double checked the trivial stuff as well, like the convergence testing for

*k mesh*,

*ecutwfc*,

*ecutrho*against hydrostatic pressure (

*tstress=.true.*), with

*degauss = 0005d0*,

*occupations='smearing'*, and

*smearing='mv'*. I used

*ibrav = 0*, since I added the cell parameters "manually".

Thanks again!

I want to perform adsorption using DFT code but I can only create nanosheet like structure - supercells from primitive and use them to check their adsorbing selectivity towards certain gas.

I want to know if suppose a material, for example, Cr2O3 is selective towards a gas when I test it using DFT code (3x3x1 supercell of Cr2O3) and if I create nanoparticles or nanotube out of it, how will it affect its selectivity. I am aware nanoparticles will show more sensitivity which will be advantageous for me but I don't have any idea how to create one in my DFT software (I am using Quantum ESPRESSO).

Hello everyone,

I do calculations on compounds with about 25-30 atoms (hydrogen, carbon, oxygen) and about 110 electrons in a water solvent (

*SMD*solvation model). These are optimizations and frequency calculations. I'm searching for the best reference method I could compare results with. These systems are being calculated with*B3LYP/6-311**G(d,p)*,*B3LYP/aug-cc-pVDZ*and*B3LYP/aug-cc-pVTZ*.I was thinking about

*CIS/6-311++G(d,p)*but have found it's not the best pick - it's barely accurate when calculating frequencies. So I came up with an idea to recruit*CCSD/cc-pVTZ*, though three things are running through my head:- I don't want calculations to run for more than 1 week (I do use 4 processors and 40GB; can try to increase it slightly)
- Because of the number of hydrogen bonding I find diffusion function necessary, though adding them to the reference method may demand much more time and computational resources in order to be calculated. How to bypass this problem?
- Maybe just use
*CCD/aug-cc-pVTZ*? However, how long will it be calculating? - Or just use optimized geometry from
*B3LYP/aug-cc-pVTZ*level as a starting one, and then perform*CCSD(T)/aug-cc-pVTZ*with frequency and optimization calculations.

The main problem arises from the technical features of the computer I'm using and time. What's is your opinion? Maybe use something completely different?

Thank you.

If we do full structural relaxation then the structure with defect might change its symmetry. So should we do only ionic relaxation of the defect structure and obtain energy from that?

First of all, I want to mention that I am undergraduate student and I am starting out in Vasp. I want to study the adsorption of arsenic in a primitive magnetite cell.

I have simulated magnetite and an arsenic atom several times and have had no problem converging the system.

When I tried to increase the amount of arsenic atoms in my system I get an error: "mpirun noticed that process rank 51 with PID 74058 on node compute136 exited on signal 6 (aborted)"

I asked a friend and he said it is possibly a communication problem in Vasp, so I increased the amount of NBANDS and with it NPAR and Core but the error continues. The problem is when I increase to 2, 4, and 5 atoms of arsenic. With 1 and 3 atoms of arsenic don't have problem.

Here I leave my Incar files, Kpoint.

I appreciate all the help you give me.

Incar

PREC = Accurate

ENCUT = 520

ISTART = 0

ICHARG = 2

ISIF = 2

IBRION = 2

NSW = 5

EDIFF = 1.0E-05

EDIFFG = -1.0E-04

ISMEAR = 0

SIGMA = 0.01

LREAL = False

LWAVE = True ; LCHARG = True ; LVTOT = False

NPAR = 16

NBANDS= 672

K-Points

0

Gamma

1 1 1

0 0 0

runVasp

#!/bin/bash

#SBATCH -J Nan_As2

#SBATCH -p knlcompute,Standard

## number of cores

#SBATCH -n 224

module load VASP/5.4.4

mpirun vasp

I understand I first need a properly converged system - check. Now, I need to calculate a self-consistent charge density (CHGCAR). Later I have to do a calculation with IBRION = -1, NSW =0, need to increase k points, read previous CHGCAR (ICHARG = 11), and turn symmetry off (ISYM = 0). The DOSCAR file from this 2nd calculation will have the required DoS data.

Doubts:

- Should I not calculate CHGCAR for the increased number of k points beforehand (in the 1st step). Why increase k points later?
- I don't understand the exact role of turning symmetry off.
- So which should it be (and why?):

- Step 1 -
**less**k points, symmetry**ON**. Step 2 -**more**k points, symmetry**OFF**, IBRION = -1, NSW = 0, ICHARG = 11 - Step 1 -
**less**k points, symmetry**OFF**. Step 2 -**more**k points, symmetry**OFF**, IBRION = -1, NSW = 0, ICHARG = 11 - Step 1 -
**less**k points, symmetry**OFF**. Step 2 -**more**k points, symmetry**ON**, IBRION = -1, NSW = 0, ICHARG = 11 - Step 1 -
**more**k points, symmetry**ON**. Step 2 -**same number**of k points, symmetry**OFF**, IBRION = -1, NSW = 0, ICHARG = 11 - Step 1 -
**more**k points, symmetry**OFF**. Step 2 -**same number**of k points, symmetry**OFF**, IBRION = -1, NSW = 0, ICHARG = 11 - Step 1 -
**more**k points, symmetry**OFF**. Step 2 -**same number**of k points, symmetry**ON**, IBRION = -1, NSW = 0, ICHARG = 11

If we want to uniaxially strain a structure incrementally, and calculate the corresponding uniaxial stress at every strain point, how should we use the VASP output files for this purpose? I have some confusion regarding this, can someone who has done this extend some help regarding the procedure?

I am designing a gas molecule-limonene using Quantum ESPRESSO. In the input file for Quantum ESPRESSO, I have to define the choice of bravais lattice and cell dimension and cell parameters. But since it is a gas molecule, it doesn't make sense. I have the exact coordinates of atoms in the molecule and hence self-consistency calculation can be run but the choice of cell parameters is causing different results. I have no idea about it and neither did I find any literature regarding the DFT calculation of my gas molecule i.e. limonene.

I had an idea of considering gas as a bunch of small simple cubic lattices with each molecule residing inside the single cell with the dimension of ~655.7 A (at ~20 C), calculated using the density and molar mass. But calculation can't be run over this big dimension.

I am attaching my input and output file. Can anyone help me out?

Hi dear all,

I just carrying out a computational run of a single point energy at MP2/6-31g++(2p,2d)//B3LYP/6-31g++(d,p), but when I tried to do the refinement at MP2/6-31g++(2p,2d) the next error appear in my log file:

Is it a problem with the integration of method or memory of my CPU? Thanks a lot. Julián.

*"Disk-based method using OVN memory for 31 occupieds at a time.*

*Estimated scratch disk usage= 2478105962 words.*

*Actual scratch disk usage= 2477844842 words.*

*JobTyp=2 Pass 1: I= 1 to 31 NPSUse= 5 ParTrn=T ParDer=T DoDerP=F.*

*Erroneous write. Write -1 instead of 1470464.*

*fd = 4*

*orig len = 1875968 left = 1470464*

*g_write"*

To calculate Band Gap Edges we need either workfunction, Band gap centre or absolute electronegativity and they have a same formula structure, what is relation between these three and why am I getting different values of band gap edges with these parameters(I should get same values). Also, if Band Gap Centre is calculated by Ev and Ec why would I again calculate Ev and Ec because I am getting same result, so is there any other method to calculate Band Gap Centre.

Hello,

I am trying to explore

**Phonopy**to create grenusian parameters using**Quantum Espresso**. I tried to create geneusian parameters and finally thermal conductivity but there is some mismatch with experimental results.I have one major query :

- Which Pseudopotential must be used to proceed ?

*If anyone using Phonopy with Quantum Espresso kindly let me know.*

Thanks,

Abhinav Nag

My system has inversion symmetry. Therefore, I'm calculating the optical transition for a material which is allowed when parities of conduction band (CB) and valence band (VB) are different (there is some finite probability for it), otherwise it is zero. I have obtained the WAVEDERF file that contains some band number (occupied and unoccupied) with specific energy, and real and imaginary part of dipole transition matrix elements. I want to plot (K-path/K-points vs. optical transition probability), but do not know how to obtain this from WAVEDERF file.

Any help would be appreciated.

I am working on a project and presently I would like to determine various nanoparticle sizes of metal/alloy clusters and slab models. How can I determine the sizes of these NPs. Can Material studios, VESTA, or Avogadro package be suitable for this purpose?

Thanks for your answers.