[DFTB-Plus-User] Questions about compiling DFTB+MPI-NEGF and running 2D Carbon Material Tutorial

yh46 yh46 at rice.edu
Tue Nov 7 05:01:32 CET 2017

Thank you very much!


Quoting Ben Hourahine <benjamin.hourahine at strath.ac.uk>:

> Dear Yuefei,
> On 06/11/17 00:20, yh46 wrote:
>> Hello Dear friends,
>> I was compiling DFTB+ on a server, the version is r4729 or r4732. The
>> source codes are in a file named 'dftb+mpi-negf.r4732', but when I
>> compile the code and run the binary dftb+, it tells me it is '
>> Unofficial release (r4729)'. So I am not sure about the version.
> The number comes from the version software control software used for
> that branch of the code. The revisions r4729 and r4732 are essentially
> the same (there are minor cosmetic changes in some printed message).
>> First question is about compiling, I saw 3 README files in the
>> directory: README, README.PARALLEL and README.NEGF, respectively. When
>> I followed the README.NEGF to compile the code, there were some
>> SEGMENTATION FAULT while running, happening both when I use single
>> core or multiple cores. So I compiled the code again without the
>> instructions in README.NEGF or README.PARALLEL, used
>> /sysmakes/make.x86_64-linux-ifort as template and changed some links
>> to library according to my system. Then I successfully compiled and it
>> can run some transport calculation from the autotest directories. It
>> can also run on multiple cores. In the output, I saw ' INIT MPI-NEGF
>> ON           4 NODES', so I think it is doing the job parallel.
>> So does that mean the compiled dftb+ binary has both MPI and NEGF
>> extension? It is quite confusing because I didn't follow README.NEGF.
>> So is it decided by the source code, and no matter what setting you
>> use in the makefile, you will get both MPI and NEGF?
> The NEGF code is constructed on top of a version of the MPI code. Both
> codes are MPI parallel, but the main difference for compilation is that
> the NEGF code can also use OpenMP parallelism for some operations (this
> is the reason for the extra -openmp flags).
> If you have compiled dftb+mpi-negf.r4732 successfully using an MPI aware
> Fortran compiler, this should contain the NGEF routines (mpif90 is a
> wrapper for the usual compiler but adds in options specific for MPI).
>> Second question is that when I use this to run the 'Tutorial:
>> Electronic Structure and Electron Transport in 2D Carbon Materials'
> [cut]
>> So why would the output files be missing or not correctly written?
>> Thank you very much!
> It seem that you probably have an earlier version of the source code
> than some of the features used in the tutorial. I'm less familiar with
> this part of the code, so off hand don't know at which version number
> these features were added here.
> Regards
> Ben
> --
>       Dr. B. Hourahine, SUPA, Department of Physics,
>     University of Strathclyde, John Anderson Building,
>             107 Rottenrow, Glasgow G4 0NG, UK.
>     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
> 2013/14 THE Awards Entrepreneurial University of the Year
>       2012/13 THE Awards UK University of the Year
>    The University of Strathclyde is a charitable body,
>         registered in Scotland, number SC015263

Yuefei Huang
Graduate Student
Department of Material Science and NanoEngineering
Rice University
email: yuefei.huang at rice.edu
phone: +1-832-499-9169

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