The ABINIT Users Mailing List ( CLOSED )

[Deyu Lu <dylu@ucdavis.edu>]

On Fri, 2006-07-14 at 10:14 +0200, Fabien Bruneval wrote:
> and also which compiler ?
> Fabien

The processor is Intel(R) Xeon(TM) CPU 3.00GHz running redhat linux.
The binary code of Abinit 4.6.5 is abinitbin_ifc_seq-4.6.5.
Abinit 5.1.2 is compiled locally with ifort.

>Which pseudo potentials are you using?
>PMA

Silicon and Hydrogen pseudo potential are generated through FHi98pp.
The headers of the PSP are the following:

hydrogen, fhi98PP : Trouiller-Martins-type, LDA Perdew/Wang (1992), l= 0
  1.000  1.000    021003              zatom,zion,pspdat
   6         7    0   0    387     0  pspcod,pspxc,lmax,lloc,mmax,r2well

silicon, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder
Perdew/Wang (1992), l= 0 local
 14.000  4.000    021003              zatom,zion,pspdat
   6         7    2   0    495     0  pspcod,pspxc,lmax,lloc,mmax,r2well

Tests have been done on bulk silicon lattice constant as well as
dielectric matrix. Bond length has been checked for hydrogen molecule.
Comparison has been made on Si-Si and Si-H bond lengths as well as Kohn-
Sham HOMO-LUMO gap in SiH4 and Si5H12 with existing reports. I see good
agreement.

The problem I encountered might be the result of out of memory since I
only have 2G memory. I 'll do some tests about it.

Deyu


> 
> Anglade Pierre-Matthieu wrote:
> > Hi,
> > 
> > Which pseudo potentials are you using?
> > 
> > PMA
> > 
> > On 7/14/06, dylu@ucdavis.edu <dylu@ucdavis.edu> wrote:
> > 
> >> I apologize if people received this message twice, since I didn't
> >> post the original message properly to the forum.
> >> -----------------------------------------------------------------------
> >> Dear Abinit users:
> >> I'm running GW calculations for silicon cluster Si5H12 placed in simple
> >> cubic supercells of 25 a.u.^3. The KSS file is generated in job 1
> >> (epsilon1.in) with ecut=15 Ha in a Gama point GS calculation, where 500
> >> bands expanded in the full planewave basis set (43387 PWs) were stored.
> >> When I tried job 2 (epsilon2.in) to compute epsilon^-1 matrix and sigma,
> >> the job crashed. Abinit 4.6.5 gave an error message "Segmentation fault
> >> (core dumped)" while reading the KSS file. Although Abinit 5.1.2 managed
> >> to finish the epsilon^-1 calculation and output the SCR file, the
> >> subsequent calculations on sigma failed with the following error message
> >> "forrtl: severe (174): SIGSEGV, segmentation fault occurred" with the
> >> last a few lines in the log file as the following:
> >> --------------------------------------------------------------------
> >> cvxclda: rhohxc returned Exc[n_val] = -9.5730 [Ha]
> >> and <Vxc[n_val]> = -0.0519 [Ha]
> >>
> >>
> >> vxc(1:3,1:3)=
> >> (-0.3894028,-9.3494627E-31) (0.0000000E+00,0.0000000E+00)
> >> ---------------------------------------------------------------------
> >> Is there any suggestions on this problem? (The input files are
> >> attached.)
> >>
> >> Many thanks
> >> Deyu Lu
> >> -------------------------------------------------------------------------------
> >>  
> >>
> >> epsilon1.ini
> >> # Si5H12 in a SC box
> >>
> >> acell 25 25 25
> >>
> >> ecut 15.0 # Maximal kinetic energy cut-off, in Hartree
> >>
> >> # Definition of the SCF procedure
> >> toldfe 1.0d-10 # Will stop when this tolerance is achieved on total 
> >> energy
> >> istwfk 1
> >> nband 500
> >> nstep 99 # Maximal number of SCF cycles
> >>
> >> # Definition of parameters for the calculation of the KSS file
> >> #nbandkss -1 # Number of bands in KSS file (-1 means the maximum
> >> possible)
> >> #npwkss 1365 # Corresponding to 1.516 Ha
> >> nbandkss 500
> >> kssform 3
> >>
> >> #Definition of the atom types
> >> ntypat 2 # There are 2 types of atom
> >> znucl 14 1 # 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 only type is Hydrogen.
> >> natom 17 # There are two atoms
> >> typat 5*1 12*2 # Silicon: 1-5; Hydrogen: 6-17
> >>
> >> #Definition of the k-point grid
> >> nkpt 1 # Only one k point is needed for isolated system,
> >> # taken by default to be 0.0 0.0 0.0
> >> diemac 1.0 # Although this is not mandatory, it is worth to
> >> # precondition the SCF cycle. The model dielectric
> >> diemix 0.5 # function used as the standard preconditioner
> >> # is described in the "dielng" input variable section.
> >> # Here, we follow the prescriptions for molecules
> >> # in a big box
> >>
> >> #Definition of the atoms
> >> xcart 0.0 0.0 0.0 # EXP Si-H bond length 2.797 Bohr (1.48 A)
> >> 2.5168172178E+00 -2.5168172178E+00 -2.5168172178E+00
> >> -2.5168172178E+00 2.5168172178E+00 -2.5168172178E+00
> >> -2.5168172178E+00 -2.5168172178E+00 2.5168172178E+00
> >> 2.5168172178E+00 2.5168172178E+00 2.5168172178E+00
> >> 4.1600819556E+00 -4.1600819556E+00 -9.1988967829E-01
> >> 4.1600819556E+00 -9.1988967829E-01 -4.1600819556E+00
> >> 9.1988967829E-01 -4.1600819556E+00 -4.1600819556E+00
> >> -9.1988967829E-01 4.1600819556E+00 -4.1600819556E+00
> >> -4.1600819556E+00 9.1988967829E-01 -4.1600819556E+00
> >> -4.1600819556E+00 4.1600819556E+00 -9.1988967829E-01
> >> -4.1600819556E+00 -4.1600819556E+00 9.1988967829E-01
> >> -4.1600819556E+00 -9.1988967829E-01 4.1600819556E+00
> >> -9.1988967829E-01 -4.1600819556E+00 4.1600819556E+00
> >> 9.1988967829E-01 4.1600819556E+00 4.1600819556E+00
> >> 4.1600819556E+00 9.1988967829E-01 4.1600819556E+00
> >> 4.1600819556E+00 4.1600819556E+00 9.1988967829E-01
> >>
> >> # Use only symmorphic operations
> >> symmorphi 0
> >> ------------------------------------------------------------------------
> >>
> >> epsilon2.ini
> >> # Si5H12 in a SC box
> >> # convergence test against ecuteps
> >>
> >> ndtset 10
> >> udtset 5 2
> >> acell 25 25 25
> >> #ecut 15.0
> >> ecut 3.5
> >> istwfk 1
> >>
> >> # DATASET 1: Calculation of the screening (epsilon^-1 matrix)
> >> optdriver?1 3
> >> getkss 1
> >>
> >> npwwfn11 1503 #1503 1.579
> >> npwwfn21 2109 #2109 2.021
> >> npwwfn31 2969 #2969 2.527
> >> npwwfn41 3431 #3431 2.779
> >> npwwfn51 3911 #3911 3.032
> >> nband?1 150
> >> nsheps 25 #25 305 0.537
> >> #nqptdm 1
> >> #qptdm 0.000010 0.000020 0.000030
> >>
> >> #DATASET 2: Calculation of the Self-Energy matrix elements (GW 
> >> corrections)
> >>
> >> optdriver?2 4
> >> getscr?2 -1
> >> npwwfn?2 3911
> >> npwsigx?2 3911
> >> nband?2 150
> >> nkptgw 1
> >> kptgw 0.000 0.000 0.000
> >> bdgw 14 18
> >>
> >> # GW calculation general parameters
> >> ppmfrq 4.3 eV
> >>
> >> #Definition of the atom types
> >> ntypat 2 # There are 2 types of atom
> >> znucl 14 1 # 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 only type is Hydrogen.
> >> natom 17 # There are two atoms
> >> typat 5*1 12*2 # Silicon: 1-5; Hydrogen: 6-17
> >>
> >> #Definition of the k-point grid
> >> nkpt 1 # Only one k point is needed for isolated system,
> >> # taken by default to be 0.0 0.0 0.0
> >> diemac 1.0 # Although this is not mandatory, it is worth to
> >> # precondition the SCF cycle. The model dielectric
> >> diemix 0.5 # function used as the standard preconditioner
> >> # is described in the "dielng" input variable section.
> >> # Here, we follow the prescriptions for molecules
> >> # in a big box
> >>
> >> #Definition of the atoms
> >> xcart 0.0 0.0 0.0 # EXP Si-H bond length 2.797 Bohr (1.48 A)
> >> 2.5168172178E+00 -2.5168172178E+00 -2.5168172178E+00
> >> -2.5168172178E+00 2.5168172178E+00 -2.5168172178E+00
> >> -2.5168172178E+00 -2.5168172178E+00 2.5168172178E+00
> >> 2.5168172178E+00 2.5168172178E+00 2.5168172178E+00
> >> 4.1600819556E+00 -4.1600819556E+00 -9.1988967829E-01
> >> 4.1600819556E+00 -9.1988967829E-01 -4.1600819556E+00
> >> 9.1988967829E-01 -4.1600819556E+00 -4.1600819556E+00
> >> -9.1988967829E-01 4.1600819556E+00 -4.1600819556E+00
> >> -4.1600819556E+00 9.1988967829E-01 -4.1600819556E+00
> >> -4.1600819556E+00 4.1600819556E+00 -9.1988967829E-01
> >> -4.1600819556E+00 -4.1600819556E+00 9.1988967829E-01
> >> -4.1600819556E+00 -9.1988967829E-01 4.1600819556E+00
> >> -9.1988967829E-01 -4.1600819556E+00 4.1600819556E+00
> >> 9.1988967829E-01 4.1600819556E+00 4.1600819556E+00
> >> 4.1600819556E+00 9.1988967829E-01 4.1600819556E+00
> >> 4.1600819556E+00 4.1600819556E+00 9.1988967829E-01
> >>
> >> # Use only symmorphic operations
> >> symmorphi 0
> >>
> > 
> >