ABINIT Discussion Forums

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...

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

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...

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

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?

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

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...

Dear Maki,

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

Best regards,

Igor

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...

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...

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 ...

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...

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...

Hi!

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

Best regards,

Igor

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...

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

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...

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...

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...

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

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...

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....

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

Hi! This is what one can find on abinit input variables part of the web Alternatively to rprim, directions of dimensionless primitive vectors can be specified by using the input variable angdeg. This is especially useful for hexagonal lattices (with 120 or 60 degrees angles). Indeed, in order for sy...

Hi! It's a good idea how to change the distance between the atoms. But you to modify it a little. You lack the increase in 'y' and 'z' coordinates (xcart+). So, what you need is xcart: -0.5 0.0 0.0 0.5 0.0 0.0 xcart+ 0.025 0.0 0.0 But even this way you wouldn't obtain what you wanted, since this wil...