ABINIT Discussion Forums

Hello: On the ABINIT website page titled "LDA density files for the Hirschfeld atomic charge analysis" (m), there appears to be a broken link for the element lanthanum. Clicking on that box gives a "550 Failed to change directory" error. I would very much appreciate if someone co...

Hello: I have been running a geometry optimization (ionmov 3 and optcell 2) on two systems which only differ by the identity of one element. In both cases, it is very difficult to converge the electronic scf of the initial geometry, so that the nstep limit is reached before the stopping tolerance (t...

Hello: My system admin has told me that Abinit 6.8.2 requires a common scratch space on our cluster if I run a job across multiple nodes. I'm wondering if the more recent version of Abinit parallelization allows a job to run across multiple nodes with just the local scratch space of each node separa...

Hello: Is there a way to specify a range for an input variable when using multiple data sets? For example, I want to run 100 different data sets from the same input file, where 50 runs are with element 1 and the other are with element 2. Instead of writing typat1 1 typat2 1 ... typat49 1 typat50 2 t...

Thank you, David!
-Kale

Hello: I have been receiving the following warning from some of my calculations: mkdenpos : WARNING - Density went < 0 at 24 points and was set to 1.00E-14. Lowest was -0.36E-04. Likely due to too low boxcut or too low ecut for pseudopotential core charge. scfcv : after setvtr, energies%e_hartree= 0...

I figured out that there was a problem with my input file, which made my atoms much too close together. That is why it seemed like so many kpoints were necessary.

Hello: I am running a calculation with the elements sodium, germanium, and gold, and it seems that the value of kptrlen is very small even with too many kpoints. My unit cell is fairly large, but with a grid of over 100 kpoints (simple gamma-centered mesh), the kptrlen is still ~10. I suspect that t...

Dear ahmad:

I think that using this command from the terminal will install gfortran on your computer, but you will need to be the root user:

yum install gcc-gfortran


Hope that helps,
Kale

Dear Payam Norouzzadeh: I'm not sure what is wrong with your input file, but I think it would be easier for you to use ABINIT's symmetry builder instead of using Mercury to get the atom positions. For example: brvlatt -1 !Abinit will convert your input to a primitive unit cell spgroup 221 acell 5.0 ...

Thank you for your reply. The dimensions of this particular cell are about 9x9x9 angstroms. The k-points grids I used were simple gamma-centered 3x3x3, 5x5x5, ..., 9x9x9 meshes. It sounds like I may need to use a high kptrlen, so my number of k-points is not so unreasonable after all. Thanks again, ...

Hello: My ABINIT calculations have been very slow, and I think I may be using too many k-points. For every calculation that I run, I use multiple sets of k-points to check that the total energy is converged with respect to the number of k-points (to within 0.1 kcal/mol). An example is below: nkpt | ...

The primitive vectors in my calculations are indeed the default unity matrix, which I think is why they were not printed in the output.

Hello Bamgbose, M. K: I find that the easiest way to determine rprim and xcart is to find the structure I want in the International Crystal Structure Database and use that information. Since the ICSD reports the conventional unit cell and ABINIT uses the primitive unit cell, you would need to set br...

Hello: Is there a reason that ABINIT would ever not print the values of the rprim variable at the end of a calculation in the log/out file? This has been happening to me recently, but it never occured before. I am wondering if means that rprim are the default values, but it seems that ABINIT usually...

Dear brehmj: These are just some wild guesses: 1) Do you have the line "spgroup 129" in your input file? 2) Are you using "brvltt -1", which says that you are using the coordinates of the conventional unit cell from the ICSD instead of the primitive cell that ABINIT uses internal...

Hello: I have received this warning in my log file, but it doesn't make sense to me because nelect_occ and zval are equal. Is there a reason that I am getting this warning? Thank you, Kale chkneu: nelect_occ= 0.12400000E+03, zval= 0.12400000E+03, and input value of charge= 0.00000000000000E+00, nele...

Dear Sheleon,

Thank you for letting me know what the problem was. I'm glad that you figured it out!
-Kale

Dear ahmad, Here is a description of the shiftk paramter: m. It has to do with how the k-points are sampled in reciprical space. In general, you can find documention about any ABINIT parameter by clicking "Input variables" on the ABINIT home page. Does that answer your question? If you are...

Hello jahangiril,

Here is a description of wtk: http://www.abinit.org/documentation/hel ... s.html#wtk

If that doesn't help, could you provide a little more detail about your problem?

Finally, do you know about the ABINIT tutorials? Those might be useful, especially if you are just getting started. (http://www.abinit.org/documentation/hel ... lcome.html)

Regards,
Kale

Dear Sheleon, You're very welcome. When you get the error message about 'N' atoms, is 'N' a number or the letter N? I tried a dummy calculation (same geometry but wrong elements and some arbitrary parameters) just now with spgroup 194, and it seemed to work with natom = 8. It can be confusing becaus...

Hello: I am trying to optimize the geometry of a crystal with 118 atoms in the unit cell with ionmov = 2. Unfortunately, this is exceedingly slow using the number of planewaves and k-points that seems necessary to get converged results, as described in the tutorials. My question is, is it worthwhile...

Dear Sheleon, Have you tried using the geometry builder with symmetry? To do this, I would use these input parameters: acell angdeg 90 90 120 spgroup 194 brvltt -1 natom natrd 2 typat znucl xred 1/3 2/3 -0.1 1/3 2/3 0.177 !Kristallografiya (1956) 1, p537-p541 where acell has the dimensions of the co...

Hello: Is there any documentation about the findmin warning? I am getting warnings that look like this, and I'm not sure whether they compromise my results or not: findmin : WARNING - The 2nd degree equation has no positive root (choice=4). findmin : COMMENT - There is a problem, since the new total...

Hello:

I can't find it now, but I recall that there is a way to run a job so that it only outputs the estimated memory requirements (and some other things) without doing any calculations. Is there an input variable option to do this?

Thank you!
Kale