[DFTB-Plus-User] R: Cannot calculate transport
Alessandro Pecchia
alessandro.pecchia at ismn.cnr.it
Thu Apr 16 09:56:49 CEST 2015
Hi Alessandro,
I also never managed to compile using “-ipo”. I just content myself with “-ip” that should make inter-procedural optimization within modules. Compilation is also much faster. In the past, when “-ipo” flag was working, I never observed a performance improvement.
Concerning negf algorithm itself, I always managed to obtain convergence at 0-bias.
You can play with the value of delta (the default is 1e-5 eV in dftb) or, frequently more effective, a temperature.
Especially if there are narrow gap states.
On the other hand, under non-equilibrium, the number of points along the real axis are critical for convergence.
The default should be fine, but in case of troubles you can increase it.
Convergence become more and more critical as your system size increases (long nanowires).
Good computations!
Alex
Da: dftb-plus-user-bounces at mailman.zfn.uni-bremen.de [mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] Per conto di Alessandro Pirrotta
Inviato: mercoledì 15 aprile 2015 18:58
A: User list for DFTB+ related questions
Oggetto: Re: [DFTB-Plus-User] Cannot calculate transport
Dear Argo,
Thank you very much for your email and your tips but none of those fixed the problem.
Dear Gabriele,
Thank you for your email.
The second paragraph of the trouble shooting (executing "ulimit -t unlimited" right before running dftb+)
fixes the problem. Now the program runs. Is that something that should not happen on a correctly compiled dftb+?
I tried to compiling again using these flags ( -ipo -O3 -no-prec-div -xP ) as suggested on the intel forum but I could not compile it correctly. I got an extremely long list of : ipo_out4.f:(.text.hot000d3+0x33df): undefined reference to ..... "
Regards,
Alessandro
Alessandro Pirrotta
PhD student
Faculty of Science
Department of Chemistry &
Nano-Science Center
University of Copenhagen
Universitetsparken 5, C321
2100 Copenhagen Ø
Denmark
DIR +45 21 18 11 90
MOB +45 52 81 23 41
alessandro.pirrotta at chem.ku.dk
<mailto:alessandro.pirrotta at gmail.com> alessandro.pirrotta at gmail.com
<http://www.ki.ku.dk/> www.ki.ku.dk
On 15 April 2015 at 14:33, Gabriele Penazzi <penazzi at uni-bremen.de> wrote:
Hi Alessandro,
have you checked if the system stack setting is responsible for this? (see troubleshooting section in the manual and this link https://software.intel.com/en-us/articles/intel-fortran-compiler-increased-stack-usage-of-80-or-higher-compilers-causes-segmentation-fault)?
Gabriele
On 04/15/2015 01:47 PM, Alessandro Pirrotta wrote:
Dear DFTB+ users,
I have compiled and successfully tested (with autotest) dftb+mpi-negf.
I have then run a drain, source and device calculation.
Drain and source run fine, but then the device calculation crashes giving this output:
Reading SKF file
....
.....
Done.
Processed input in HSD format written to 'dftb_pin.hsd'
Starting initialization...
--------------------------------------------------------------------------------
PGRID:ALLPROC: 1 x 1
PGRID:ATOM: 1 x 1
Poisson parallelized on 1 nodes
Atomic density tolerance: 1.000000000000000E-005
Atomic density cutoff: 9.39669825812203 a.u.
Input PoissonBox= 30.0000 30.0000 30.0000 A
PoissAcc= 1.000000000000000E-007
Bulk Boundary Potential: No
Atomic cutoff radius= 4.97251893391611 A
CENTRAL REGION
Atom start - end = 1 22
CONTACT # 1
Atom start - end = 23 118
direction: 3
Fermi Level= -4.70500000000000 eV
mu= 0.136056922500000 V
CONTACT # 2
Atom start - end = 119 214
direction: -3
Fermi Level= -4.70500000000000 eV
mu= -0.136056922500000 V
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
INIT MPI-NEGF ON 1 NODES
CPU 0 READY
PRINTING CPU: T
Mode: Static calculation
Contact upload: Yes
Contact calculation: No
Use Poisson solver: Yes
Self consistent charges: Yes
SCC-tolerance: 0.100000E-06
Max. scc iterations: 2000
Ewald alpha parameter: 0.000000E+00
Spin polarisation: No
Nr. of up electrons: 1091.000000
Nr. of down electrons: 1091.000000
Periodic boundaries: No
Diagonalizer: Green's Functions (density matrix)
Maximal SCC-cycles: 2000
Electronic temperature: 0.100000E-07
Initial charges: Set automatically (system chrg: 0.000E+00)
Included shells: S: s, p, d
C: s, p
O: s, p
H: s
Au: s, p, d
Extra options:
--------------------------------------------------------------------------------
********************************************************************************
** Geometry step: 0
********************************************************************************
MAXNEIGHBORS: 161
Structure info:
Number of PLs: 1
Interacting PLs: 1 1
iSCC Total electronic Diff electronic SCC error
=========================================================================
SOLVING POISSON EQUATION
=========================================================================
-------------------------------------------------------------------------
Poisson Box internally adjusted:
x range= -14.93910 15.06090; Periodic: F
y range= -15.02760 14.97240; Periodic: F
z range= -3.14441 15.18553; Periodic: F
Mesh details:
Lx= 30.000 nx= 129 dlx= 0.23437
Ly= 30.000 ny= 129 dly= 0.23437
Lz= 18.330 nz= 65 dlz= 0.28641
-------------------------------------------------------------------------
-------------------------------------------------------------------------
Relative Poisson Error = 1.952627165542703E-008
Number of cycles executed = 8/ 60
-------------------------------------------------------------------------
*************************************************************************
=========================================================================
COMPUTING DENSITY MATRIX
=========================================================================
CONTOUR INTEGRATION:*** 70 points
srun: error: node244: task 0: Segmentation fault (core dumped)
srun: Terminating job step 615175.0
I have compiled it with mpif90, ifort 13.0.1, and openmpi-1.6.5-i4
Any idea why the tests run fine and this does not?
Kind regards,
Alessandro
Alessandro Pirrotta
PhD student
Faculty of Science
Department of Chemistry &
Nano-Science Center
University of Copenhagen
Universitetsparken 5, C321
2100 Copenhagen Ø
Denmark
DIR +45 21 18 11 90 <tel:%2B45%2021%2018%2011%2090>
MOB +45 52 81 23 41 <tel:%2B45%2052%2081%2023%2041>
alessandro.pirrotta at chem.ku.dk
<mailto:alessandro.pirrotta at gmail.com> alessandro.pirrotta at gmail.com
<http://www.ki.ku.dk/> www.ki.ku.dk
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Dr. Gabriele Penazzi
BCCMS - University of Bremen
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