ABINIT Discussion Forums

Thanks for reporting the problem and fixing the bug. I have to say that the two options eph_task = -2, 2 are not very well documented. Let's try to clarify the main purpose of these two options. eph_task = +2 is mainly used to produce a netcdf file with the matrix elements <k+q,b'|d/d_p V_scf| k, b>...

The last line in the log file before the calculation terminates is always: - Creating HDf5 file with MPI-IO support: tmp/den_o_GSR.nc The problem is not necessarily due to the output of the GSR file. In your log file, I find the following section: - Creating HDf5 file with MPI-IO support: tmp/den_o...

When given the option by Cut3D of which output file type I'd like, which one should I select?

Vesta can read volumetric data in Xcrysden format (xsf)

However I am having difficulties trying to use it with Abinit. set_fermie_to_vbm is an AbiPy function that recomputes the Fermi energy by finding the highest occupied state in the KS energies stored in the GSR.nc file. In the case of NSCF calculations, indeed, the Fermi energy reported in the GSR f...

#5 0x7fdce98e909a in ??? #6 0x55f5910f5d03 in __m_cgtools_MOD_cg_zgemv at ../../../src/44_abitools/m_cgtools.F90:898 This part of the backtrace indicates that SIGILL is raised by ZGEMV (matrix-vector multiplication provided by openblas). I would suggest to recheck the compilation of openblas and th...

Can you try to increase the value of boxcutmin from 2 to e.g. 4? We found some difference when comparing Abinit DFPT phonons with phonopy finite difference method with Abinit forces and we managed to make the phonopy results agree with DFPT by increasing boxcutmin. BTW: Are you using ADDGRID=True (h...

Im using verison 7.4.3 as i mentioned before, i also checked for the typo and there was not any.

I don't think the posdoppler input variable is available in v 7.4.3.
I would suggest to use a more recent Abinit version.

Do you have any idea about accuracy in calculating forces of abinit?

The cutoff energy and the converge criterion used to stop the SCF cycle can affect the quality of the forces
but it's hard to say without looking at your input file.

I am a little confused about if my supercell is charged or not when I introduce the defects. If I remove a Cd atom to introduce the Cd Vacancy, will my supercell be charged by default (given that Cd is the cation in CdTe)? No, the unit cell is always charge-neutral unless you use the charge input v...

Hi Samuel, the input file works in sequential on my laptop. The max memory allocated on the heap is ~700 Mb that is consistent with the value reported by Abinit at the beginning. Perhaps it's a problem with the stack triggered by automatic arrays. Did you try to increase the stack size limit with e....

When trying to use MPI level 3 (--with-mpi-level=3) the build crashes. I don't think this option has some effect at the level of the source code except for making the compilation abort! The build system automatically detects whether the MPI library provides the mpi module (MPI2+) or if we have to f...

The tarball available on github do not contain the configure script
One has to generate it by executing ~abinit/config/scripts/makemake (requires python).

Does anyone know of a flag for gfortran to make it more lenient (like before) or how I can circumvent this without recoding all of the abinit interfaces.

With gfortran > 10, you need to add --fallow-argument-mismatch to your compiler options

No, unfortunately the EPH code and A-TDEP are not interfaced with each other.

Dear Jack, My work flow for dealing with phonon symmetries is below. I hope it can help some people. Many thanks for sharing your expertise with ISODISTORT. 1) Perform your Abinit DFPT phonon calculation and calculate the band structure with anaddb, using a version with NetCDF. 2) Load the *PHBST.nc...

Parallelism of DFPT works on k-points and bands by default, without parallel_kgb. This means that you have to first spread the k-points on CPU and if you can put more start to spread over bands. When I say "spread" I mean that you just have to choose the number of CPU in your mpirun calculation and...

Abinit can only read UPF1 files, the UPF2 format is not supported. Moreover it's not possible to use PAW or Ultrasoft pseudopotentials from QE, even if they are given in UPF1 format. For PAW calculations with Abinit, you can use the JTH table available at http://www.pseudo-dojo.org/ Abinit and QE im...

Well, the error message is pretty self-explanatory:

Input natom must be defined, but was absent for dataset 0
Action: check the input file.

so the question is "did you check your input file?".

Can you run the same input file without mpirun.

Can you post the output of `abinit -b`.
This error is usually seen when abinit has been compiled without MPI.

Avoid mixing FFTW3 with MKL as MKL provides wrappers for fftw3 calling the intel DFTI FFT library.
This means that the linker will receive multiple definitions for the same procedure and
results are unpredictable!
Either use MKL for linalg and fft or FFTW3 with e.g. openblas for linalg.

The packages used in building abinit are netCDF MKL (within Intel 19.3) FFTW3 (3.3.8) Avoid mixing FFTW3 with MKL as MKL provides wrappers for fftw3 calling the intel DFTI FFT library. This means that the linker will receive multiple definitions for the same procedure and results are unpredictable!...

This is the section used by our test suite to run the automatic tests, you can safely ignore it.
Actually, all the lines starting with `#` are ignored by the parser.

I believe the error message is self-explanatory: you need to set the value of pawecutdg in the input file to run PAW calculations.

I would suggest to read the PAW tutorials and the documentation of pawecutdg before running PAW calculations.

Very likely you didn't activate support for netcdf while configuring the package For the AbiPy documentation: https://github.com/abinit/abipy#about Note that the majority of the post-processing tools available in AbiPy require output files in netcdf format so we strongly suggest to compile Abinit wi...