The ABINIT Users Mailing List ( CLOSED )

[Vahid Askarpour <vaskarpour@yahoo.com>]

Dear Professor Gonze,

The changes you suggested resulted in successful AIM runs.

Thanks for your help.

Vahid Askarpour



----- Original Message ----
From: Xavier Gonze <xavier.gonze@uclouvain.be>
To: forum@abinit.org
Sent: Thu, January 14, 2010 9:46:00 AM
Subject: Re: [abinit-forum] AIM segmentation fault (core dumped)

Dear Vahid Askarpour,

The bug is in the routine initaim.F90 . You should replace the line 274 
(well, in the latest developer's version,
but this has likely not changed much from your version) :

& llg2(ngfft(3)),llg3(ngfft(3)),cdig1(ngfft(1)-1),cdig2(ngfft(2)-1),&

by

& llg2(ngfft(2)),llg3(ngfft(3)),cdig1(ngfft(1)-1),cdig2(ngfft(2)-1),&

The only difference is the change of a 3 by a 2 for character 14 of this 
line...

Best,
Xavier


On 23 Dec 2009, at 19:30, Vahid Askarpour wrote:

> Dear Abinit Users,
> 
> Running AIM (ABINIT 5.8.4) on two different clusters (one using Intel 
> compilers, the other PGI compilers), I get segmentation fault on both. I 
> have allocated 10GB for the task. The stack trace suggests a problem 
> freeing or deallocating memory. Earlier, there was a similar report on the 
> Forum but the issue was never resolved. I have used two ecut values of 15 
> and 25 Ha but I got the same results. Here are the two input files, one for 
> generating the density file, the other for bader analysis:
> 
> File 1
> ------------------------------------------------------------------------------------------
> # Crystalline 8HI
> occopt  6
> tsmear  0.01
> #Definition of the k-point grids
> kptopt 1          # Option for the automatic generation of k points, taking
>                   # into account the symmetry
> nshiftk 1
> shiftk  0.0 0.0 0.0  # These shifts will be the same for all grids
> ngkpt   8 8 8
> #Definition of the SCF procedure
> nstep 200          # Maximal number of SCF cycles
> toldfe 1.0d-6    # between two consecutive evaluations of total energy
>                   # differ by less than toldfe (in Hartree)
> diemac 12       # Although this is not mandatory, it is worth to
>                   # precondition the SCF cycle. The model dielectric
>                   # function used as the standard preconditioner
>                   # is described in the "dielng" input variable section.
>                   # Here, we follow the prescription for bulk silicon.
> # Data common to the three different datasets
> # Definition of the unit cell: Triclinic
> acell 1.3652185228E+01  1.9310062579E+01  9.8097544562E+00
> angdeg 90.00000116  90.00000117  44.99121644
> strtarget -4.75846d-4 -4.75846d-4 -4.75846d-4 0 0 0
> strprecon 0.1
> # Definition of the atom types
> ntypat  2         # There are two types of atom
> znucl 1 53         # The keyword "znucl" refers to the atomic number of the
>                   # possible type(s) of atom. The pseudopotential(s)
>                   # mentioned in the "files" file must correspond
>                   # to the type(s) of atom. Here, the type is H and I.
> # Definition of the atoms
> natom 16          # There are 16 atoms
> typat  1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2   # They  are of two types , that 
> is, H and I.
> xcart         4.4575393774E+00  1.9054055331E+00  1.1215044142E+01
>               9.4739271732E-01 -1.5347641011E+00  1.1215042652E+01
>               9.6571747909E-01  5.3983758496E+00  1.1215046211E+01
>              -2.4756193134E+00  1.8892786634E+00  1.1215044134E+01
>               4.4186330990E+00  1.8664452803E+00  6.3101667787E+00
>               7.8599773549E+00  5.3755345569E+00  6.3101627548E+00
>               4.4369740034E+00  8.7995863589E+00  6.3101642197E+00
>               9.2681947032E-01  5.3594230855E+00  6.3101687934E+00
>              -2.5251165030E+00 -1.5831110203E+00  1.1215016651E+01
>               4.5164792687E+00 -1.5906794232E+00  1.1215014128E+01
>               4.5172363318E+00  5.4567912155E+00  1.1215012544E+01
>              -2.5302436040E+00  5.4584964054E+00  1.1215015663E+01
>               8.6712054180E-01  1.8080285220E+00  6.3101375466E+00
>               7.9146019343E+00  1.8063244617E+00  6.3101372695E+00
>               7.9094736823E+00  8.8479293887E+00  6.3101379406E+00
>               8.6788045533E-01  8.8555031864E+00  6.3101381586E+00
> # Definition of the planewave basis set
> ecut 25.0          # Maximal kinetic energy cut-off, in Hartree
> ---------------------------------------------------------------------------------------------------------
> 
> File2
> ------------------------------------------------------------------------------------------------------
> surf 1
> crit 2
> atom 1
> gpsurf 1
> irho 1
> ivol 1
> inpt 150
> ntheta 48
> nphi 48
> atrad 1.0
> radstp 0.03
> ratmin 0.80
> maxatd 10.0
> maxcpd 10.0
> ---------------------------------------------------------------------------------------------------
> I'd appreciate any suggestions.
> 
> Gratefully,
> 
> Vahid Askarpour
> Dalhousie University,
> Halifax, Canada
> 
> 
>