Search found 271 matches

by ilukacevic
Wed May 03, 2017 11:21 am
Forum: Input file
Topic: How to relax atomic systems in only one direction? [SOLVED]
Replies: 2
Views: 688

Re: How to relax atomic systems in only one direction? [SOLVED]

Dear Visum, Yes, there is. Please, look at the variables http://www.abinit.org/doc/helpfiles/for-v8.2/input_variables/html_automatically_generated/varrlx.html#natfixx http://www.abinit.org/doc/helpfiles/for-v8.2/input_variables/html_automatically_generated/varrlx.html#iatfixx and similar for other d...
by ilukacevic
Thu Apr 13, 2017 9:02 am
Forum: Input file
Topic: Visualizing
Replies: 2
Views: 843

Re: Visualizing

Dear Fatemeh,

You can use cut3D utility provided in your abinit package. It will format your density file for specific usage (you choose from the list). Then you can plot it. I usually use gnuplot or Wolfram Mathematica.

Best regards,

Igor
by ilukacevic
Thu Apr 06, 2017 8:51 am
Forum: Input file
Topic: How to vary distance between two atoms out of many
Replies: 1
Views: 498

Re: How to vary distance between two atoms out of many

Dear Mawla, Well, this is more a geometry question rather than abinit. I don't think you can change one Pd-Si distance without changing the other Pd-Si distances or the Si-Si distances in the same time. So, you will have to choose which one of these suits you the most. The pyramid volume will change...
by ilukacevic
Thu Apr 06, 2017 8:36 am
Forum: Input file
Topic: How to relax only neighboring atoms [SOLVED]
Replies: 2
Views: 804

Re: How to relax only neighboring atoms [SOLVED]

Dear Mawla,

You can use 'natfix' and 'iatfix' variables to specify exactly which atoms you want to fix. The ones you do not specify will be relaxed.

Best regards,

Igor
by ilukacevic
Tue Apr 04, 2017 8:56 am
Forum: Theory
Topic: PLOT [SOLVED]
Replies: 2
Views: 1918

Re: PLOT [SOLVED]

Dear Asadi, There is more than one way in which to proceed after you obtain the EIG file. One is to use the readband.py script which can be found inside the abinit package. It will read your EIG file and format it for usage in xmgrace. The bands will be in columns. You will still have to edit the hi...
by ilukacevic
Tue Mar 21, 2017 8:13 am
Forum: Input file
Topic: InGaSb properties
Replies: 3
Views: 829

Re: InGaSb properties

I cannot see any problem in your files file. How do you know that you have a problem? Do you get some kind of error in the log file?
by ilukacevic
Mon Mar 20, 2017 8:17 am
Forum: Input file
Topic: InGaSb properties
Replies: 3
Views: 829

Re: InGaSb properties

Dear Uness,

Please, refer first to the Tutorials given on the abinit web

http://www.abinit.org/doc/helpfiles/for-v8.2/tutorial/welcome.html

After that you might have some specific questions, which can be more easily answered.

Best regards,

Igor
by ilukacevic
Fri Mar 17, 2017 8:25 am
Forum: Pseudopotentials and PAW datasets
Topic: GaAs wurtzite
Replies: 21
Views: 10986

Re: GaAs wurtzite

Dear shalom, As everyone else who started using abinit, you should first and foremost read the abinit specific documentation available on the web site. After that, before starting to calculate your system(s), you should go through the first 4 tutorials (more if you have time). There you will find mo...
by ilukacevic
Tue Dec 27, 2016 9:56 am
Forum: Ground state
Topic: SCF convergence problem in vacancy defect modelling
Replies: 4
Views: 1543

Re: SCF convergence problem in vacancy defect modelling

Dear Maki,

Did you try increasing some of these variables: npulayit, nnsclo or nline in combination with iscf 7 or 17?

Best regards,

Igor
by ilukacevic
Wed Dec 14, 2016 8:53 am
Forum: Ground state
Topic: how to constrain magnetization in ABINIT? [SOLVED]
Replies: 2
Views: 1081

Re: how to constrain magnetization in ABINIT? [SOLVED]

Dear ucsdmavrl, For magconon 1, you constrain only the direction of a vector, while its size will be left open for 'relaxation' during the energy minimization. For magconon 2, you constrain both the direction and the size of the vector, and the energy is minimized under both of these conditions. The...
by ilukacevic
Thu Dec 01, 2016 8:51 am
Forum: Ground state
Topic: Applying strain on a 2 D material [SOLVED]
Replies: 2
Views: 1158

Re: Applying strain on a 2 D material [SOLVED]

Dear manik, 1. It seems that you misunderstood something. Strain concerns the deformation of lattice (through rprim variable), not atomic positions (xcart). If you followed the elastic response function tutorial at http://www.abinit.org/doc/helpfiles/for-v8.0/tutorial/lesson_elastic.html#4 you could...
by ilukacevic
Tue Nov 22, 2016 8:13 am
Forum: Response calculations
Topic: Wrong PDOS for NiTi [SOLVED]
Replies: 1
Views: 1871

Re: Wrong PDOS for NiTi [SOLVED]

Dear disae, 1. First, this is not phonon DOS, but phonon dispersion curves. 2. The differences you see can be the result of many factors: approximation used in the calculation, unconverged calculation parameters, unrelaxed structure, and similar. There are many things you should check first, before ...
by ilukacevic
Tue Oct 18, 2016 8:53 am
Forum: Input file
Topic: doping changes the space group symmetry [SOLVED]
Replies: 3
Views: 1911

Re: doping changes the space group symmetry [SOLVED]

Dear Espiridion, With doping you are changing the symmetry of the structure (the original atom is replaced by the dopant). So, naturally, the space group changes. If you already knew that, maybe you could "hack" abinit or some parts of it to keep the symmetry. But some of the elders will k...
by ilukacevic
Tue Sep 13, 2016 8:26 am
Forum: Ground state
Topic: fatbands for ncpp
Replies: 4
Views: 1678

Re: fatbands for ncpp

I don't know if there is a variable which will 'directly' give you the atom species decomposed DOS. Some of the 'elders' probably know better. I do it by using prtdos 3 to obtain the l decomposed DOS for each atom. Then I add all the l contribution for each atom and get what you asked for. Expect 'e...
by ilukacevic
Mon Sep 12, 2016 9:02 am
Forum: Ground state
Topic: fatbands for ncpp
Replies: 4
Views: 1678

Re: fatbands for ncpp

Hi!

You can do it yourself using Xmgrace, for example. You just plot the contribution as errors represented as symbol sizes.

Best regards,

Igor
by ilukacevic
Fri Sep 02, 2016 8:46 am
Forum: Post-processing Tools
Topic: Free Energies from ANADDB [SOLVED]
Replies: 1
Views: 1724

Re: Free Energies from ANADDB [SOLVED]

Dear ckunka, Indeed, you cannot obtain thermal properties from this kind of calculation. It calculates only the phonons at the Gamma point, which is not enough. For the thermal properties one need the phonon DOS, and for that one needs to sample the phonons throughout the BZ (as in RF2 tutorial). Th...
by ilukacevic
Thu Jul 07, 2016 8:26 am
Forum: Theory
Topic: Total energy increases for more k points [SOLVED]
Replies: 7
Views: 6450

Re: Total energy increases for more k points [SOLVED]

Hi!

Can you copy here your input file?

Best regards,

Igor
by ilukacevic
Fri Jul 01, 2016 8:36 am
Forum: Pseudopotentials and PAW datasets
Topic: pseudopotentials for graphene
Replies: 4
Views: 3303

Re: pseudopotentials for graphene

Hi!

Since you have about a zillion reference to compare to ;) , the best way would be to test several pseudopotentials, available at the abinit web site, and see which one agrees the best (with those references) concerning the property you are interested in.

Best regards,

Igor
by ilukacevic
Thu Jun 23, 2016 9:43 am
Forum: Response calculations
Topic: Raman spectrum
Replies: 2
Views: 2311

Re: Raman spectrum

Hi! In these two papers, for example, you can find the procedure how to calculate Raman spectrum from the Abinit output data. GEOPHYSICAL RESEARCH LETTERS, VOL. 33, L12S05, doi:10.1029/2006GL025736, 2006 PRB 71, 214307 (2005) There's a lot of post-processing involved. And have in mind that only inte...
by ilukacevic
Thu Mar 17, 2016 9:42 am
Forum: Response calculations
Topic: something wrong with the phonon caused imaginary freq
Replies: 11
Views: 4897

Re: something wrong with the phonon caused imaginary freq

If you obtained the required pressure at the end of the 1st dataset of your RF calculation, then you are using the correct wavefunction. But since your frequencies are still negative, it means that there is a physical problem in the simulated system taking into account the used approximations (xc, p...
by ilukacevic
Wed Mar 16, 2016 1:26 pm
Forum: Response calculations
Topic: something wrong with the phonon caused imaginary freq
Replies: 11
Views: 4897

Re: something wrong with the phonon caused imaginary freq

Very much possible. It is known that in some systems phonon frequencies become imaginary at high pressures. You could have the same situation. Try to solve first the problem of different pressures in relaxation and RF calculations. If all you input variables are the same, then you should get the sam...
by ilukacevic
Wed Mar 16, 2016 12:56 pm
Forum: Response calculations
Topic: something wrong with the phonon caused imaginary freq
Replies: 11
Views: 4897

Re: something wrong with the phonon caused imaginary freq

That might be the source of your problem.

Did you insert the relaxed acell into your RF input file? I see from the inputs your provided in your first post that the acell in the RF input file is the same as in the relaxation input file. If you used that RF input file, you should change acell.

Igor
by ilukacevic
Tue Mar 15, 2016 8:41 am
Forum: Response calculations
Topic: something wrong with the phonon caused imaginary freq
Replies: 11
Views: 4897

Re: something wrong with the phonon caused imaginary freq

Hi! 1] Before anything else, you have to make sure that all common variables have the same values in both calculations. And I can see that some of them do not, like ngkpt, etc. Also it is advised to use the same energy tolerance criterion, while you use toldff in the relaxation and tolvrs in RF. Bec...
by ilukacevic
Wed Jan 27, 2016 8:39 am
Forum: Input file
Topic: ngkpt convergence
Replies: 1
Views: 865

Re: ngkpt convergence

Hi! All obtained values should be compared with the most converged one. In your case with the one for mesh 14x14x1. If you take the usual Etot tolerance of 5x10^(-4) Ha, then your converged value would be the one for 7x7x1. The only question remains is whether 14x14x1 is a completely converged mesh....
by ilukacevic
Mon Nov 16, 2015 8:08 am
Forum: Pseudopotentials and PAW datasets
Topic: InAs band structure
Replies: 18
Views: 12922

Re: InAs band structure

Hi!

1] What do you mean by converged the lattice parameters?

2] It looks like typical bands obtained with unconverged ecut and/or ngkpt. Did you converge the energy bands wrt these two parameters?

Best regards,

Igor