Dear Bibhas, The error message is self-explanatory. The contour integration would benefit by adding 5 more energy points without increasing the computational load. However this is not an error, just a suggestion. The error is in your atomic coordinates. I am unable to open your included files, but most likely you have atomic coordinates that are outside the unit cell. For example, you could have negative z coordinates or x or y values that go beyond the unit cell vectors. For band structure calculation you don't have to worry about this since the system is periodic, but for transport you do. The message even tells you how to fix the problem. Just add the suggested block to shift all atomic coordinates automatically, so you don't have to fix it atom by atom.
Good luck! Leo 2017-10-20 5:10 GMT-02:00 Bibhas Manna <[email protected]>: > Dear Transiesta Users, > > I am very new to run the transiesta code. I have successfully computed > .TSHS file for the left electrode at the first step. Assuming that my right > and left electrodes are equivalent, I then move on to run the scattering > region file using .TSHS for left electrode as an input. However, I faced > some fatal errors related to transiesta run. Errors are as follows: > > ************************ Begin: TS CHECKS AND WARNINGS > ************************ > Without loosing performance you can increase the equilibrium integration > precision. > You can add 5 more energy points in the equilibrium contours, for FREE! > This is 5 more energy points per chemical potential. > 5(1=-1) 7(1=-1) > atom(cell-dir=neighbour-cell) > *** Device atomic coordinates are not inside unit-cell. > *** This is a requirement for bias calculations > as the Poisson equation cannot be correctly handled > due to inconsistencies with the grid and atomic coordinates > *** Will continue, but will die when running V /= 0 *** > Electrode: Left lies outside the unit-cell. > Please shift the entire structure using the following recipe: > If you already have AtomicCoordinatesFormat, add these > AtomicCoordinatesFormat Ang > %block AtomicCoordinatesOrigin > 1.6556 0.0009 0.0000 > %endblock AtomicCoordinatesOrigin > ************************ End: TS CHECKS AND WARNINGS > ************************** > > **************************************** > TRANSIESTA REPORTED IMPORTANT WARNINGS > **************************************** > > ****************************** > TRANSIESTA REPORTED ERRORS > ****************************** > One or more errors have occured doing transiesta initialization, check the > output > Stopping Program from Node: 0 > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 CREATE > FROM 0 > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > > > I have tried to find the origin of such errors but failed every time. > > Please suggest me with some solution for this problem. Any help in this > regard is highly appreciable. > I am also attaching my input and output file of scattering region for your > kind consideration. > > Thanking you. > With regards, > Bibhas > > > > > > > > >
