Search found 398 matches

by ebousquet
Mon Jul 06, 2020 2:58 pm
Forum: Input file
Topic: Calculation of energy for NaFeO2 (triclinic setting)
Replies: 2
Views: 952

Re: Calculation of energy for NaFeO2 (triclinic setting)

How to build the input file for a crystal is explained in the tutorials of Abinit. Now, which pseudos and which functional to be used, one can look at the literature to see what has been used before. Here, Fe is probably magnetic such that PAW and DFT+U should probably used with PBEsol for example. ...
by ebousquet
Mon Jul 06, 2020 2:54 pm
Forum: Response calculations
Topic: Full DFPT of Raman Scattering
Replies: 1
Views: 44

Re: Full DFPT of Raman Scattering

Dear John,
A first basic question that you might have done but did you merge all the DDB files outputed during your calculation (with mrgddb)? It looks indeed strange that your main calculation has done it but the anaddb program is complaining that it is not there.
Best wishes,
Eric
by ebousquet
Mon Jul 06, 2020 2:48 pm
Forum: Configuration
Topic: Linking 6 computers in a cluster
Replies: 1
Views: 8

Re: Linking 6 computers in a cluster

Dear athenawang ,
I think this is beyond Abinit user question and you have low chance to get a response (but we never know!), you should ask your question to a more dedicated "IT" forum...
Best wishes,
Eric
by ebousquet
Mon Jul 06, 2020 2:45 pm
Forum: Input file
Topic: The use of magnetic moment, kpoints, ionmov, supercells, and DOS
Replies: 4
Views: 111

Re: The use of magnetic moment, kpoints, ionmov, supercells, and DOS

the array [3, natom] for the spinat, does it represent 3 coordinates and number of atoms according to xred? In my case I have 30 atoms and have set the magnetic moment to 4 for the Mn positions along the z-coordinate. spinat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 #Mn atoms 0 0 4 0 0 4 0 0 4 0 0 ...
by ebousquet
Mon Jul 06, 2020 2:31 pm
Forum: Input file
Topic: out of memory
Replies: 5
Views: 149

Re: out of memory

Dear Suman, A general comment: you use a grid of k-point of 1x8x8 and your cell parameters a, b and c are 28 ,37 and 40 respectively. This does not make sense becauase the k-point length is inversely proportional to the cell length such that having 1 kpoint for 28 Bohr and 8 for 37 and 40 is inconsi...
by ebousquet
Wed Jun 10, 2020 11:49 am
Forum: Input file
Topic: Parallelization and convergence
Replies: 18
Views: 576

Re: Parallelization and convergence

I was hoping to get 0.2% ~ 0.1eV accuracy, but this may not be practical. Then, according to your convergence test, you have to use a large enough ecut to reach this precision... There is an oscillation in the tolvrs and toldfe values in the output file. Also, there is an oscillation in the vacuum ...
by ebousquet
Wed Jun 10, 2020 8:56 am
Forum: Input file
Topic: Non primitive cells, space groups
Replies: 3
Views: 110

Re: Non primitive cells, space groups

OK, great!
The symrel are indeed duplicated with a translation vector that you can see in the output file through tnons.
Best,
Eric
by ebousquet
Wed Jun 10, 2020 8:45 am
Forum: Input file
Topic: SCF cycle is not starting
Replies: 6
Views: 179

Re: SCF cycle is not starting

I have 16 gB RAM and a quad core i7(I installed with make mj4 but still shows 1 proc during calculations, but I assume it still uses 4 since it is relatively fast), but would like to use the GPU cores later if possible. Right now I don't know really how to install the GPU support. I would need help...
by ebousquet
Wed Jun 10, 2020 8:32 am
Forum: Input file
Topic: Using spgroup correctly
Replies: 5
Views: 177

Re: Using spgroup correctly

Dear Eric So you mean that I have to list all atoms in the unit cell at all times? I thought the spgroup was able to use symmetry operators and construct the whole cell by providing the Wyckoff positions of the assymetric cell. Yes, you have to list all atoms of the unit cell, Abinit does not recon...
by ebousquet
Mon Jun 08, 2020 9:36 am
Forum: Input file
Topic: Using spgroup correctly
Replies: 5
Views: 177

Re: Using spgroup correctly

Dear ssh77,
Abinit works with the unit cell and not the asymmetric unit cell (i.e. with only minimal Wyckoff sites) such that you have to list all the atoms of the unit cell and not the asymmetric ones. Well, I guess this is your problem.
Best wishes,
Eric
by ebousquet
Mon Jun 08, 2020 9:27 am
Forum: Input file
Topic: Phase transition under pressure?
Replies: 4
Views: 124

Re: Phase transition under pressure?

Dear Nawzad, In your case, I would check the phonon dispersions of the cubic 5 atom cell at different pressure to check whether you have an instability or not. If no instability is present, it will mean that the cubic phase is indeed stable in your calculation. If an instability appears (reported as...
by ebousquet
Mon Jun 08, 2020 9:23 am
Forum: Input file
Topic: SCF cycle is not starting
Replies: 6
Views: 179

Re: SCF cycle is not starting

Dear ssh77,
You are running a calculation with 80 atoms on a laptop?? How many CPU and RAM do you have, this is a big calculation that would require a multicore-job to get it running within a decent time...
Best wishes,
Eric
by ebousquet
Fri Jun 05, 2020 11:01 am
Forum: Input file
Topic: Non primitive cells, space groups
Replies: 3
Views: 110

Re: Non primitive cells, space groups

Dear Jerkov, You need to analyze the relaxed cell with a program that will tell you the exact crystal space group in the case of supercell calculation. Abipy or qAgate are directly interfaced with Abinit and can do the job through the spglib python library. You can also use the FINDSYM software from...
by ebousquet
Fri Jun 05, 2020 10:56 am
Forum: Response calculations
Topic: Phonon DOS
Replies: 19
Views: 655

Re: Phonon DOS

Dear Jerkov, OK, you have included the asr, it is not the problem then. If only the points in between the main q-points at which you did the DFPT are giving strange negative results it might means that the q-grid is not large enough to have a good interpolation. You used 2x2x2 q-grid, which night no...
by ebousquet
Thu Jun 04, 2020 4:07 pm
Forum: Pseudopotentials and PAW datasets
Topic: Potential problem with Lu JTH v1.1
Replies: 1
Views: 60

Re: Potential problem with Lu JTH v1.1

Dear Andrew,
Thank you for your report.
In any case, the user should always check convergence and validity of the pseudo used, even in the case of a often used pseudo, it is possible that it fails in the specific conditions of your system.
Best wishes,
Eric
by ebousquet
Thu Jun 04, 2020 4:04 pm
Forum: Input file
Topic: ipcel issue
Replies: 1
Views: 47

Re: ipcel issue

Hi kittysoman2013,
Did you check other parameters like diemix, diemac before iprcell?
Best wishes,
Eric
by ebousquet
Thu Jun 04, 2020 4:03 pm
Forum: Input file
Topic: Phase transition under pressure?
Replies: 4
Views: 124

Re: Phase transition under pressure?

Dear Nawzad, If you constrain the cell with acell, then you compute the internal energy at constrained strain and not at hydrostatic pressure. This is important mostly when the system is not cubic since the constrain along a,b and c will not represent the same pressure. I guess this can be your prob...
by ebousquet
Thu Jun 04, 2020 3:58 pm
Forum: Input file
Topic: Input file contents
Replies: 1
Views: 37

Re: Input file contents

Dear ssh77,
These extra lines are for internal automatic tests of Abinit, you can disregard them.
Best wishes,
Eric
by ebousquet
Thu Jun 04, 2020 3:57 pm
Forum: Input file
Topic: out of memory
Replies: 5
Views: 149

Re: out of memory

Dear Suman
Abinit has almost no limit on the number of atoms, 100 is clearly not a problem.
Could it be that your computer does not have enough RAM memory for this calculation?
Best wishes,
Eric
by ebousquet
Thu Jun 04, 2020 3:54 pm
Forum: Input file
Topic: U determination for oxygen monoclinic ?
Replies: 1
Views: 35

Re: U determination for oxygen monoclinic ?

Dear kittysoman2013, Once you add chkprim=0, I'm not sure you can still use the spgroup flag. Your error message is a segmentation fault such that it can be difficult to know its origin (memory allocation problem). Looking at your input I see that you did not initialized all the flags for +U, you ha...
by ebousquet
Thu Jun 04, 2020 3:48 pm
Forum: Response calculations
Topic: polarization
Replies: 4
Views: 144

Re: polarization

Dear Suman, You should look at the link dbennett1994 gave you (and Stengel reference given there) regarding calculation of Polarization because once you play with hetero-structures, slabs, etc, the proper variable to look at should be D. Additionally, computing P requires to have a zero reference an...
by ebousquet
Thu Jun 04, 2020 3:38 pm
Forum: Response calculations
Topic: Recalculating electronic polarization from ground state orbitals and orbitals differentiated with respect to k
Replies: 2
Views: 82

Re: Recalculating electronic polarization from ground state orbitals and orbitals differentiated with respect to k

Dear Kevin, I'm not sure if I understand, but you want to compute the polarization through the Berry phase, I guess you did it with berryopt=-1 with Abinit, right? Now, you have to be careful with quantum of polarization problem, see for example: http://palata.fzu.cz/abinitschool/download/We3_polari...
by ebousquet
Thu Jun 04, 2020 3:31 pm
Forum: Input file
Topic: SCF cycle is not starting
Replies: 6
Views: 179

Re: SCF cycle is not starting

Dear ssh77, I ran your input and everything goes through fine after reading the psp files, so I don't know what can be your problem. Can it be a memory problem (the job takes 6-7 Gb)? Regarding the ixc, if you don't specify a value there, it'll be read directly from the pseudo file and set automatic...
by ebousquet
Thu Jun 04, 2020 3:19 pm
Forum: Input file
Topic: Xred for 2d Material such as MoS2, Be2C
Replies: 3
Views: 78

Re: Xred for 2d Material such as MoS2, Be2C

I don't know if Jmol can do it but you can use the new software qAgate which is interfaced with Abinit and can do the job.
To install it, you can do:

Code: Select all

sudo add-apt-repository ppa:piti-diablotin/abiout
sudo apt-get update
sudo apt install -y qagate
Best wishes,
Eric
by ebousquet
Thu Jun 04, 2020 3:17 pm
Forum: Input file
Topic: Parallelization and convergence
Replies: 18
Views: 576

Re: Parallelization and convergence

Dear Eliezer, OK, it sounds like you can get easily an error bar of 1% but going lower is CPU time demanding. At this stage you need to know if 1% precision on the WF is enough for you? If so, ecut=16-20 look good. There is something making a noise oscillation but I don't know what can be the origin...