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Re: [abinit-forum] Input & Log file for inspection

From: "Anglade Pierre-Matthieu" <anglade@gmail.com>
To: forum@abinit.org
Subject: Re: [abinit-forum] Input & Log file for inspection
Date: Fri, 16 Nov 2007 08:53:39 +0100
Domainkey-signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta; h=received:message-id:date:from:to:subject:in-reply-to:mime-version:content-type:references; b=e/2Vr2Yqjkkcej/Btcn2YR0ZU3Ekh6aYN1D687fDIls7zQApsIOUDNaAKJAbTj+t7mEcxB13UKXPobiWAP1UGmAhaU+WYhKadeq5yfYMtY0KshtfPqsCJ02Rx4w19I1oe+3iPmAwXY84ZjWC0ojE/nZxi3e9yz7TEWobK4X889Y=

Hello,

Given the size of your cell it is possible that you run into an integer overflow problem.
It is also possible that the version of gfortran you use is too old and is a "prerelease" although part of a gcc release.
Endly thee may be other problem (I'm going to try some test with you input but I'm only running a 1.6GHz pentium-M with 512 MB of RAM).
I would advise:
1) check if your gfortran is older than 6 month. If so you must update it and recompile Abinit. But in this cas I can't understand how Abinit passes its tests.
2) Try to compile Abinit with the option: -fdefault-integer-8
This is not conform to fortran standards but may solve your problem.

Looking at your input I feel there are some weird points:
- your ecut is really low for an 11 e- pseudopotential of Gold.
- Your k-point mesh is not perfectly fitted to your cell shape. Are you sure it is the best you can get ?
- If your cell is what it looks like (I have not plotted atom position but I guess you have something like a cube of Gold with a layer of vacuum along one face), For the relaxation of the surface layer you can use much less atom. And this will be useful because Plane-wave codes sclae like N^3 ...
- You will likely not have enough bands to get a converge results. For safety you can use nband=2*Ne- for a first run and then reduce to the numbre of band really needed. But hte default number will likely be too low.

regards

PMA

On Nov 16, 2007 6:34 AM, <ramirez_o273@utpb.edu> wrote:

Dear PMA,
I'm running on a Dell Xeon (CPU 3.60 GHz & 3 GB RAM) with Abinit version 5.4.3. I'm also working with a Au LDA pseudopotential from FHI code downloaded from the Abinit website. I'm also using a gfortran compiler.

Input:

#############################################
#This input file was created on 11/13/07
#Purpose: To relax the first two layers.

#Geometry
acell 32.69793114 32.69793114 60.91532164 #Given in Bohrs, see Step1.in for the Angstrom values

rprim 1 0 0 0 1 0 0 0 1
ntypat 1
znucl 79
natom 252
typat 252*1
xred
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-1.8095128013E-01 9.0828180087E-01 0.0000000000E+00
-9.7613130673E-02 8.2494365141E-01 -3.1630215604E-01
-9.7613130673E-02 8.2494365141E-01 -1.8976268031E-01
-9.7613130673E-02 8.2494365141E-01 -6.3254226771E-02
-1.8095128013E-01 1.0749580998E+00 -3.7955638281E-01
-1.8095128013E-01 1.0749580998E+00 -2.5304792927E-01
-1.8095128013E-01 1.0749580998E+00 -1.2650845354E-01
-1.8095128013E-01 1.0749580998E+00 0.0000000000E+00
-9.7613130673E-02 9.9161995032E-01 -3.1630215604E-01
-9.7613130673E-02 9.9161995032E-01 -1.8976268031E-01
- 9.7613130673E-02 9.9161995032E-01 -6.3254226771E-02
-1.8095128013E-01 1.2416343987E+00 -3.7955638281E-01
-1.8095128013E-01 1.2416343987E+00 -2.5304792927E-01
-1.8095128013E-01 1.2416343987E+00 -1.2650845354E-01
-1.8095128013E-01 1.2416343987E+00 0.0000000000E+00
-9.7613130673E-02 1.1582962492E+00 -3.1630215604E-01
-9.7613130673E-02 1.1582962492E+00 -1.8976268031E-01
-9.7613130673E-02 1.1582962492E+00 -6.3254226771E-02

#Stating which atomic positions are to stay fixed
natfix 180 #Number of atomic positions to fix
iatfix
1
2
3
5
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#Definition of the k-point grid
kptopt 1
ngkpt 8 8 1
nshiftk 2
shiftk 0.5 0.0 0.0
0.0 0.5 0.0

#The relaxation
optcell 0 #acell & rprim stay fixed, but atomic positions move
ionmov 3
tolmxf 5.0d-5
ntime 10

#Definition of occupation numbers
occopt 4
tsmear 0.04
iprcel 45 #Preconditioner

#Definition of the planewave basis set
ecut 6

#Definition of the SCF procedure
nstep 10 # Maximal number of SCF cycles
toldff 5.0d-5
#Exchange-correlation functional
ixc 7

Log File:

ABINIT

Give name for formatted input file:
Step1red.in
Give name for formatted output file:
Step1red.out
Give root name for generic input files:
stpi
Give root name for generic output files:
stpo
Give root name for generic temporary files:
stmp

.Version 5.4.3 of ABINIT
.(sequential version, prepared for a i686_linux_UNKNOWN computer)

.Copyright (C) 1998-2007 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).

ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .

.Starting date : Thu 15 Nov 2007.

- input file -> Step1red.in
- output file -> Step1red.out
- root for input files -> stpi
- root for output files -> stpo

instrng : 477 lines of input have been read

iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 1 , psp file is 79-Au.LDA.fhi
read the values zionpsp= 11.0 , pspcod= 6 , lmax= 3

iofn2 : deduce mpsang = 4, n1xccc = 0.

invars1m : enter jdtset= 0
ingeo : takes atomic coordinates from input array xred

symanal : COMMENT -
The Bravais lattice determined only from the primitive
vectors, bravais(1)= 4, is more symmetric
than the real one, iholohedry= 2, obtained by taking into
account the atomic positions.
symspgr : the symmetry operation no. 1 is the identity
symplanes : the symmetry operation no. 2 is a mirror plane
symspgr : spgroup= 6 Pm (=Cs^1)
getkgrid : length of smallest supercell vector (bohr)= 3.699349E+02
Simple Lattice Grid
symkpt : found identity, with number 1
invars1: mkmem undefined in the input file. Use default mkmem = nkpt
invars1: With nkpt_me= 32 and mkmem = 32, ground state wf handled in core.
invars1: mkqmem undefined in the input file. Use default mkqmem = nkpt
invars1: With nkpt_me= 32 and mkqmem = 32, ground state wf handled in core.
invars1: mk1mem undefined in the input file. Use default mk1mem = nkpt
invars1: With nkpt_me= 32 and mk1mem = 32, ground state wf handled in core.

Symmetries : space group Pm (# 6); Bravais mP (primitive monocl.)
invars2: take the default value of fband= 1.25000000E-01
getkgrid : length of smallest supercell vector (bohr)= 3.699349E+02
Simple Lattice Grid
symkpt : found identity, with number 1

inkpts : istwfk preprocessed, gives following first values (max. 6): 1 1 1 1 1 1
chkneu : initialized the occupation numbers for occopt= 1
spin-unpolarized case :
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
Fortran runtime error: Attempt to allocate negative amount of memory. Possible integer overflow
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
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2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00
For input ecut= 5.000000E+00 best grid ngfft= 72 72 125
max ecut= 5.112108E+00
getng: value of mgfft= 125 and nfft= 648000
getng: values of ngfft(4),ngfft(5),ngfft(6) 73 73 125
getmpw: optimal value of mpw= 34824
For input ecut= 2.216656E+00 best grid ngfft= 45 45 90
max ecut= 2.233956E+00
getng: value of mgfft= 90 and nfft= 182250
getng: values of ngfft(4),ngfft(5),ngfft(6) 45 45 90
getmpw: optimal value of mpw= 10125

getdim_nloc : deduce lmnmax = 16, lnmax = 4,
lmnmaxso= 16, lnmaxso= 4.
memory : analysis of memory needs
================================================================================
Values of the parameters that define the memory need of the present run
intxc = 0 ionmov = 3 iscf = 7 xclevel = 1
lmnmax = 4 lnmax = 4 mband = 1418 mffmem = 1
P mgfft = 125 mkmem = 32 mpssoang= 4 mpw = 34824
mqgrid = 3001 natom = 252 nfft = 648000 nkpt = 32
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 2 n1xccc = 0 ntypat = 1 occopt = 1
For the susceptibility and dielectric matrices, or tddft :
mgfft = 90 nbnd_in_blk= 178 nfft = 182250 npw = 10125
================================================================================
P This job should need less than 29739.004 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : -464.459 Mbytes ; DEN or POT disk file : 4.946 Mbytes.
================================================================================

Biggest array : f_fftgr(disk), with 79.1036 MBytes.
memana : allocated an array of 79.104 Mbytes, for testing purposes.

--
Pierre-Matthieu Anglade

Input & Log file for inspection, ramirez_o273, 11/16/2007
- Re: [abinit-forum] Input & Log file for inspection, Anglade Pierre-Matthieu, 11/16/2007
  - Re: [abinit-forum] Input & Log file for inspection, Anglade Pierre-Matthieu, 11/16/2007
- Re: [abinit-forum] Input & Log file for inspection, Xavier Gonze, 11/16/2007