using pw for Metallic systems: the case of hexagonal cells

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Re: using pw for Metallic systems: the case of hexagonal cells

Postby andrea marini » Fri Mar 27, 2009 10:59 pm

Yunfeng wrote:
I reproduced you error with yambo-3.1.2 rev. 300, that is not the most updates version.
This error has been solved in the revision 315 released on October 2008.

Dear Andrea

I was actually using "yambo-3.2.0 Revision 315". Is it right version?


In this case I cannot reproduce your problem on my Linux PC. My rev 315 coneverges The fermi level without any problem. It could be a problem of the IBM. Do you have access to a Linux machine to check whether this is the case ?

Andrea

P.S.: I am going to move this post in the "Running Yambo" section. Let's follow the discussione there.
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: using pw for Metallic systems: the case of hexagonal cells

Postby Yunfeng » Sun Mar 29, 2009 9:05 am

andrea marini wrote:
In this case I cannot reproduce your problem on my Linux PC. My rev 315 coneverges The fermi level without any problem. It could be a problem of the IBM. Do you have access to a Linux machine to check whether this is the case ?


What's the best architecture for yambo? I thought it is IBM, as you are using sp5.cineca.

I have setup Yambo in a linux cluster. I reproduced the same problem with 12x12x12 kpoint mesh.

I did the configure as follows

./configure FC=/home/sw/michelleintel/mpich2-install/bin/mpif90 --with-netdf=/home/liang/local/netcdf --enable-largedb --with-iotk=/home/liang/espresso-3.2.3/iotk --with-p2y=3.2

Then I modified the setup file to:

#====================================
# Yambo 3.2.0 r.315 setup
#====================================
#
# Main setup
#
package_string = Yambo 3.2.0 r.315
cpu = x86_64
os = linux
debug = yes
make = make
ar = ar
arflags = -ru
cc = gcc
cflags = -g -O2 -D_C_US -D_FORTRAN_US
pcc = /home/sw/michelleintel/mpich2-install/bin/mpicc
pccflags = -g -O2 -D_C_US -D_FORTRAN_US
cpp = gcc -E
cppflags = -P
f90 = /home/sw/michelleintel/mpich2-install/bin/mpif90
f90flags = -assume byterecl -O3 -tpp7 -nofor_main
f90uflags = -assume byterecl -O0 -tpp7 -nofor_main
f90suffix = .f90
pf90 = /home/sw/michelleintel/mpich2-install/bin/mpif90
pf90flags = -assume byterecl -O3 -tpp7 -nofor_main
f77 = ifort
f77flags = -assume byterecl -O3 -tpp7
f77uflags = -assume byterecl -O0 -tpp7
package_bugreport = yambo@yambo-code.org
#
# Paths
#
prefix = /home/liang/yambo/yambo-3.2.0-r.315
exec_prefix = ${prefix}/bin
srcdir = /home/liang/yambo/yambo-3.2.0-r.315
libdir = /home/liang/yambo/yambo-3.2.0-r.315/lib
libpath = -L/home/liang/yambo/yambo-3.2.0-r.315/lib
includedir = /home/liang/yambo/yambo-3.2.0-r.315/include
lblas = -lblas
llapack = -llapack
lblacs =
lscalapack =
lmpi =
lnetcdf =
iotk_dir = /home/liang/espresso-3.2.3/iotk
etsf_dir =
lfftw =

I also copied "/home/liang/espresso-3.2.3/iotk/src/*" to "/home/liang/espresso-3.2.3/iotk/"

then
make all

NB: ifort version is 9.1

Sincerely, Yunfeng
Yunfeng Liang
Department of Physics and Engineering Physics
University of Saskatchewan
116 Science Place
Saskatoon S7N0K4, SK, Canada
Email: yul059@mail.usask.ca, liangyunfeng@gmail.com
Tel: +1(306)966-6213
Fax: +1(306)966-6400
Yunfeng
 
Posts: 21
Joined: Mon Mar 23, 2009 8:25 pm

Re: using pw for Metallic systems: the case of hexagonal cells

Postby Yunfeng » Sun Mar 29, 2009 9:15 am

Another question is how to define Fermi Energy in Yambo?

In the successful circulations of 8x8x8, I noticed that the Fermi energy reported by Pwscf and Yambo is different! The former is 11.2817 eV and the latter is 11.19781 eV. Below is the input for Pwscf. (I didn't prepare an input for Yambo, so just do /home/liang/Marini/yambo-3.2.0-r.315/bin/yambo)


si.scf.in

&control
calculation = 'scf' ,
restart_mode='from_scratch' ,
prefix='silicon' ,
tstress = .true. ,
tprnfor = .true. ,
pseudo_dir = '/home/liang/PP/' ,
outdir = '/localscr/liang/tmp/Si/'
/
&system
ibrav= 4, celldm(1) =4.817,
celldm(3)=0.942, nat= 1, ntyp= 1,
ecutwfc =30.0
occupations='smearing', smearing='marzari-vanderbilt',degauss=0.020
/
&electrons
diagonalization='bfgs'
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-8
diago_full_acc = .true.
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
K_POINTS { automatic }
8 8 8 0 0 0


si.band.in


&control
calculation='bands' ,
wf_collect = .true. ,
prefix='silicon' ,
pseudo_dir = '/home/liang/PP/' ,
outdir = '/localscr/liang/tmp/Si/'
/
&system
ibrav= 4, celldm(1) =4.817,
celldm(3)=0.942, nat= 1, ntyp= 1,
ecutwfc =30.0, nbnd = 150,
nosym = .false.
/
&electrons
diagonalization='cg' ,
diago_thr_init = 1.e-6 ,
diago_full_acc = .true. ,
/
ATOMIC_SPECIES
Si 28.086 Si.pbe-rrkj.UPF
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
K_POINTS { automatic }
8 8 8 0 0 0

Sincerely, Yunfeng
Yunfeng Liang
Department of Physics and Engineering Physics
University of Saskatchewan
116 Science Place
Saskatoon S7N0K4, SK, Canada
Email: yul059@mail.usask.ca, liangyunfeng@gmail.com
Tel: +1(306)966-6213
Fax: +1(306)966-6400
Yunfeng
 
Posts: 21
Joined: Mon Mar 23, 2009 8:25 pm

Re: using pw for Metallic systems: the case of hexagonal cells

Postby Yunfeng » Sun Mar 29, 2009 9:29 am

I have printed out the energy and index. It seems that the problem is not related to the format of integer, something like I4, or I4.4.

It is just located at the part to find the Fermi Energy. By avoiding the "do while" loop for finding converged Fermi Energy, the yambo can go on and finish very fast(I mean yambo with the absence of yambo.in).

So that part (to find the Fermi Energy) is related to the compiler?
Sincerely, Yunfeng
Yunfeng Liang
Department of Physics and Engineering Physics
University of Saskatchewan
116 Science Place
Saskatoon S7N0K4, SK, Canada
Email: yul059@mail.usask.ca, liangyunfeng@gmail.com
Tel: +1(306)966-6213
Fax: +1(306)966-6400
Yunfeng
 
Posts: 21
Joined: Mon Mar 23, 2009 8:25 pm

Re: using pw for Metallic systems: the case of hexagonal cells

Postby Yunfeng » Sun Mar 29, 2009 9:38 am

The computer is IBM P5-550, running AIX Version 5.3.0.50.

The way I compiled Yambo in this IBM machine:

./configure F77=f77 CC=cc --with-netcdf=/usr/global/ibm/netcdf64/ --with-iotk='/scratch_ibm/yfliang/espresso-3.2.3/iotk' --with-p2y=3.2
gmake all

Sincerely, Yunfeng
Yunfeng Liang
Department of Physics and Engineering Physics
University of Saskatchewan
116 Science Place
Saskatoon S7N0K4, SK, Canada
Email: yul059@mail.usask.ca, liangyunfeng@gmail.com
Tel: +1(306)966-6213
Fax: +1(306)966-6400
Yunfeng
 
Posts: 21
Joined: Mon Mar 23, 2009 8:25 pm

Re: using pw for Metallic systems: the case of hexagonal cells

Postby andrea marini » Fri Apr 03, 2009 11:11 am

Dear Yunfeng,

a new version of the routine fermi_level.F has been posted in the repository (rev. 388). This version should solve your problem. Please download the latest source by using svn and check in the devel/04_03_2009 folder for the new updated source.

Let us know if the new source works.

Cheers

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: using pw for Metallic systems: the case of hexagonal cells

Postby Yunfeng » Sat Apr 04, 2009 4:16 pm

andrea marini wrote: a new version of the routine fermi_level.F has been posted in the repository (rev. 388). This version should solve your problem. Please download the latest source by using svn and check in the devel/04_03_2009 folder for the new updated source.



Dear Andrea,

Thank you very much! The Fermi_not_converged problem has been solved! With the newer patch [rev.389], the code went further and stopped at

" <24m-22s> [05] Bethe-Salpeter Kernel
[ERROR] STOP signal received while in :[05] Bethe-Salpeter Kernel
[ERROR]Fractional e/h occupations found. BS coupling forced."

For your convenience, I attached the input again

********************************************************************
# GPL Version 3.2.1 Revision 387
# http://www.yambo-code.org
#

em1s # [R Xs] Static Inverse Dielectric Matrix
optics # [R OPT] Optics
bse # [R BSK] Bethe Salpeter Equation.
bss # [R BSS] Bethe Salpeter Equation solver
BSresKmod= "xc" # [BSK] Resonant Kernel mode. (`x`;`c`;`d`,`u`)
% BSEBands
1 | 6 | # [BSK] Bands range
%
BSENGBlk= 51 RL # [BSK] Screened interaction block size
BSENGexx= 2085 RL # [BSK] Exchange components
% QpntsRXs
1 | 133 | # [Xs] Transferred momenta
%
% BndsRnXs
1 | 60 | # [Xs] Polarization function bands

%
NGsBlkXs= 51 RL # [Xs] Response block size
% LongDrXs
1.000000 | 0.000000 | 0.000000 | # [Xs] [cc] Electric Field
%
BSSmod= "h" # [BSS] Solvers `h/d/i/t`
% BEnRange
0.00000 | 10.00000 | eV # [BSS] Energy range
%
% BDmRange
0.02000 | 0.80000 | eV # [BSS] Damping range
%
BEnSteps= 500 # [BSS] Energy steps
% BLongDir
1.000000 | 0.000000 | 0.000000 | # [BSS] [cc] Electric Field
%
********************************************************************

Sincerely, Yunfeng
Yunfeng Liang
Department of Physics and Engineering Physics
University of Saskatchewan
116 Science Place
Saskatoon S7N0K4, SK, Canada
Email: yul059@mail.usask.ca, liangyunfeng@gmail.com
Tel: +1(306)966-6213
Fax: +1(306)966-6400
Yunfeng
 
Posts: 21
Joined: Mon Mar 23, 2009 8:25 pm

Re: using pw for Metallic systems: the case of hexagonal cells

Postby andrea marini » Sat Apr 04, 2009 5:51 pm

Yunfeng wrote:Dear Andrea,

Thank you very much! The Fermi_not_converged problem has been solved! With the newer patch [rev.389], the code went further and stopped at

" <24m-22s> [05] Bethe-Salpeter Kernel
[ERROR] STOP signal received while in :[05] Bethe-Salpeter Kernel
[ERROR]Fractional e/h occupations found. BS coupling forced."


Dear Yungfeng,

I have moved your last post here.

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Posts: 447
Joined: Mon Mar 16, 2009 4:27 pm

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