Thanks a lot for your quick guidance, I will correct .fdf file and then do the transport caculations. Best regards, Nadia
On Fri, Jun 5, 2015 at 1:18 PM, Nick Papior Andersen <[email protected]> wrote: > You must not have an electronic temperature of zero... You need _some_ > smearing of the DOS. > > 2015-06-05 10:45 GMT+02:00 Nadia Salami <[email protected]>: > >> Dear Nick, >> .fdf file is attached. >> Thanks in advance, >> >> On Fri, Jun 5, 2015 at 1:05 PM, Nick Papior Andersen < >> [email protected]> wrote: >> >>> Provide your fdf... >>> >>> 2015-06-05 10:28 GMT+02:00 Nadia Salami <[email protected]>: >>> >>>> Dear transiesta users, >>>> >>>> Following output appears in the transiesta calculation in the parallel >>>> mode. >>>> >>>> Siesta-3.2 is used. >>>> >>>> >>>> ************************ >>>> * TRANSIESTA BEGIN * >>>> ************************ >>>> contour: Residuals: >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 1 >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 2 >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 3 >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 4 >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 5 >>>> contour: 0.00000 0.00000 0.000000000 0.000000000 6 >>>> contour: Fermi Line: >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 1 >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 2 >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 3 >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 4 >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 5 >>>> contour: 0.00000 0.00000 -0.000000000 -0.000000000 6 >>>> contour: Circle: >>>> contour: -0.00003 0.00695 NaN NaN 1 >>>> contour: -0.00072 0.03646 NaN NaN 2 >>>> contour: -0.00432 0.08894 NaN NaN 3 >>>> contour: -0.01458 0.16305 NaN NaN 4 >>>> contour: -0.03648 0.25631 NaN NaN 5 >>>> contour: -0.07549 0.36471 NaN NaN 6 >>>> contour: -0.13682 0.48238 NaN NaN 7 >>>> contour: -0.22443 0.60167 NaN NaN 8 >>>> contour: -0.34004 0.71357 NaN NaN 9 >>>> contour: -0.48241 0.80851 NaN NaN 10 >>>> contour: -0.64704 0.87763 NaN NaN 11 >>>> contour: -0.82644 0.91408 NaN NaN 12 >>>> contour: -1.01101 0.91408 NaN NaN 13 >>>> contour: -1.19041 0.87763 NaN NaN 14 >>>> contour: -1.35504 0.80851 NaN NaN 15 >>>> contour: -1.49741 0.71357 NaN NaN 16 >>>> contour: -1.61302 0.60167 NaN NaN 17 >>>> contour: -1.70063 0.48238 NaN NaN 18 >>>> contour: -1.76196 0.36471 NaN NaN 19 >>>> contour: -1.80097 0.25631 NaN NaN 20 >>>> contour: -1.82287 0.16305 NaN NaN 21 >>>> contour: -1.83313 0.08894 NaN NaN 22 >>>> contour: -1.83673 0.03646 NaN NaN 23 >>>> contour: -1.83742 0.00695 NaN NaN 24 >>>> 36 energy points >>>> 36 36 >>>> ----- DISTRIBUTION OF ENERGY POINTS AMONG PROCESSORS ----- >>>> Node Point Part Read-ins ZEnergy Weight >>>> 0 1 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 1 1 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 2 1 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 3 1 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 0 2 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 1 2 N 4 0.00000 0.00000 -0.00000 -0.00000 >>>> 2 2 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 3 2 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 0 3 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 1 3 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 2 3 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 3 3 N 4 0.00000 0.00000 0.00000 0.00000 >>>> 0 4 N 4 -0.00003 0.00695 NaN NaN >>>> 1 4 N 4 -0.00072 0.03646 NaN NaN >>>> 2 4 N 4 -0.00432 0.08894 NaN NaN >>>> 3 4 N 4 -0.01458 0.16305 NaN NaN >>>> 0 5 N 4 -0.03648 0.25631 NaN NaN >>>> 1 5 N 4 -0.07549 0.36471 NaN NaN >>>> 2 5 N 4 -0.13682 0.48238 NaN NaN >>>> 3 5 N 4 -0.22443 0.60167 NaN NaN >>>> 0 6 N 4 -0.34004 0.71357 NaN NaN >>>> 1 6 N 4 -0.48241 0.80851 NaN NaN >>>> 2 6 N 4 -0.64704 0.87763 NaN NaN >>>> 3 6 N 4 -0.82644 0.91408 NaN NaN >>>> 0 7 N 4 -1.01101 0.91408 NaN NaN >>>> 1 7 N 4 -1.19041 0.87763 NaN NaN >>>> 2 7 N 4 -1.35504 0.80851 NaN NaN >>>> 3 7 N 4 -1.49741 0.71357 NaN NaN >>>> 0 8 N 4 -1.61302 0.60167 NaN NaN >>>> 1 8 N 4 -1.70063 0.48238 NaN NaN >>>> 2 8 N 4 -1.76196 0.36471 NaN NaN >>>> 3 8 N 4 -1.80097 0.25631 NaN NaN >>>> 0 9 N 4 -1.82287 0.16305 NaN NaN >>>> 1 9 N 4 -1.83313 0.08894 NaN NaN >>>> 2 9 N 4 -1.83673 0.03646 NaN NaN >>>> 3 9 N 4 -1.83742 0.00695 NaN NaN >>>> Total no. points: 36 >>>> Total no. points to read: 36 36 >>>> ---------------------------------------------------------- >>>> Begin LEFT >>>> unit cell: >>>> 37.7945 0.0000 0.0000 >>>> 0.0000 30.2290 0.0000 >>>> 0.0000 0.0000 20.9983 >>>> Size: 291600 >>>> Left.GF already exist, will be overwritten! >>>> Efermi: 0.0000000000000000 >>>> GF: Spin number -> 1 >>>> Got LEFT Electrode GF >>>> Done >>>> Begin RIGHT >>>> unit cell: >>>> 37.7945 0.0000 0.0000 >>>> 0.0000 30.2290 0.0000 >>>> 0.0000 0.0000 20.9983 >>>> Size: 291600 >>>> Right.GF already exist, will be overwritten! >>>> Efermi: -0.0000000000000000 >>>> GF: Spin number -> 1 >>>> Got RIGHT Electrode GF >>>> Done >>>> L-ELEC: lastoL: 0 9 18 27 >>>> 36 45 54 63 72 81 90 >>>> 99 108 117 126 135 144 >>>> 153 162 171 180 189 198 >>>> 207 216 225 234 243 252 >>>> 261 270 279 288 297 306 >>>> 315 324 333 342 351 360 >>>> 369 378 387 396 405 414 >>>> 423 432 441 450 459 468 >>>> 477 486 495 504 513 522 >>>> 531 540 >>>> R-ELEC: lastoR: 0 9 18 27 >>>> 36 45 54 63 72 81 90 >>>> 99 108 117 126 135 144 >>>> 153 162 171 180 189 198 >>>> 207 216 225 234 243 252 >>>> 261 270 279 288 297 306 >>>> 315 324 333 342 351 360 >>>> 369 378 387 396 405 414 >>>> 423 432 441 450 459 468 >>>> 477 486 495 504 513 522 >>>> 531 540 >>>> TRANSIESTA: Initializing lists >>>> From SIESTA: Efermi= -3.889 >>>> qc0 : 0.000 >>>> qcn0 : 725.892 >>>> nou,NGL,NGR: 1890 540 540 >>>> TranSiesta: Qsol,Qtot: NaN 1260.000 1.000 >>>> >>>> >>>> >>>> and I have faced to the following error in the terminal. >>>> >>>> mpirun noticed that process rank 0 with PID 5436 on node salami-desktop >>>> exited on signal 11 (Segmentation fault). >>>> -------------------------------------------------------------------------- >>>> >>>> real 59m41.908s >>>> user 219m22.759s >>>> sys 0m27.482s >>>> >>>> >>>> >>>> I don' know what's the matter, and any comments and advice will be >>>> appreciated. >>>> Best, >>>> >>>> Nadia Salami >>>> >>>> >>> >>> >>> -- >>> Kind regards Nick >>> >> >> > > > -- > Kind regards Nick >
