In my opinion the electronic temperature here is not the target temperature, while the temperature used for quize-particle distribution. So the smearing is needed, otherwise the charge density is represented by delta functions from FD distribution. Dexi Shao
2015-06-05 17:02 GMT+08:00 Nadia Salami <[email protected]>: > 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 >> > >
