Search found 276 matches

by gmatteo
Thu Mar 25, 2021 2:18 am
Forum: Post-processing Tools
Topic: getwfq_filepath ignored by optdriver=7 in Abinit and other issue with eph_task = -2 [SOLVED]
Replies: 3
Views: 750

Re: getwfq_filepath ignored by optdriver=7 in Abinit and other issue with eph_task = -2 [SOLVED]

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>...
by gmatteo
Sat Mar 20, 2021 5:04 am
Forum: Input file
Topic: SCF convergence deteriorates during structural relaxation resulting in crash
Replies: 3
Views: 747

Re: SCF convergence deteriorates during structural relaxation resulting in crash

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...
by gmatteo
Tue Mar 16, 2021 12:42 am
Forum: Input file
Topic: Vesta Plot
Replies: 1
Views: 540

Re: Vesta Plot

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)
by gmatteo
Tue Mar 16, 2021 12:36 am
Forum: Post-processing Tools
Topic: Using set_fermie_to_vbm()
Replies: 1
Views: 163

Re: Using set_fermie_to_vbm()

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...
by gmatteo
Wed Jan 20, 2021 12:35 am
Forum: Platform specific questions
Topic: Running Abinit in virtual box Ubuntu [SOLVED]
Replies: 5
Views: 1523

Re: Running Abinit in virtual box Ubuntu [SOLVED]

#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...
by gmatteo
Tue Dec 29, 2020 1:22 am
Forum: Ground state
Topic: Thermal conductivity calculation using abinit+phono3py
Replies: 4
Views: 625

Re: Thermal conductivity calculation using abinit+phono3py

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...
by gmatteo
Tue Dec 22, 2020 12:54 am
Forum: Input file
Topic: Posdoppler variable missing
Replies: 3
Views: 921

Re: Posdoppler variable missing

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.
by gmatteo
Sun Dec 20, 2020 1:58 pm
Forum: Ground state
Topic: Thermal conductivity calculation using abinit+phono3py
Replies: 4
Views: 625

Re: Thermal conductivity calculation using abinit+phono3py

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.
by gmatteo
Thu Dec 10, 2020 2:24 am
Forum: Ground state
Topic: How do you calculate defect formation energies?
Replies: 3
Views: 992

Re: How do you calculate defect formation energies?

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...
by gmatteo
Wed Dec 02, 2020 9:51 pm
Forum: Input file
Topic: Molecules in Abinit [SOLVED]
Replies: 2
Views: 451

Re: Molecules in Abinit [SOLVED]

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....
by gmatteo
Tue Dec 01, 2020 4:19 pm
Forum: Build system
Topic: MPI level = 3 fails
Replies: 1
Views: 1620

Re: MPI level = 3 fails

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...
by gmatteo
Wed Oct 28, 2020 4:12 pm
Forum: Configuration
Topic: A question for 9.2.1
Replies: 3
Views: 627

Re: A question for 9.2.1

The tarball available on github do not contain the configure script
One has to generate it by executing ~abinit/config/scripts/makemake (requires python).
by gmatteo
Wed Oct 28, 2020 4:10 pm
Forum: Platform specific questions
Topic: gfortran complex/real cast complaint [SOLVED]
Replies: 4
Views: 986

Re: gfortran complex/real cast complaint [SOLVED]

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
by gmatteo
Wed Oct 14, 2020 1:28 am
Forum: Response calculations
Topic: el-ph calculations based on a-TDEP
Replies: 1
Views: 413

Re: el-ph calculations based on a-TDEP

No, unfortunately the EPH code and A-TDEP are not interfaced with each other.
by gmatteo
Thu Oct 01, 2020 5:18 am
Forum: Response calculations
Topic: symmetry of phonon modes
Replies: 17
Views: 31769

Re: symmetry of phonon modes

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...
by gmatteo
Thu Oct 01, 2020 4:35 am
Forum: Response calculations
Topic: Best parallelism for 1st order response calculations.
Replies: 3
Views: 865

Re: Best parallelism for 1st order response calculations.

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...
by gmatteo
Fri Sep 25, 2020 6:20 pm
Forum: Pseudopotentials and PAW datasets
Topic: H2 example with PAW pseudopotential and spinorbital effects
Replies: 2
Views: 1037

Re: H2 example with PAW pseudopotential and spinorbital effects

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...
by gmatteo
Tue Sep 22, 2020 11:33 pm
Forum: Input file
Topic: Tutorial base1
Replies: 1
Views: 654

Re: Tutorial base1

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?".
by gmatteo
Mon Sep 14, 2020 11:43 pm
Forum: Platform specific questions
Topic: Fortran runtime error
Replies: 1
Views: 909

Re: Fortran runtime error

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.
by gmatteo
Tue Sep 08, 2020 10:11 pm
Forum: Ground state
Topic: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
Replies: 8
Views: 3011

Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]

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.
by gmatteo
Tue Sep 08, 2020 10:04 pm
Forum: Configuration
Topic: runtest.py failed 12 tests
Replies: 2
Views: 1036

Re: runtest.py failed 12 tests

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!...
by gmatteo
Thu Jul 02, 2020 2:47 am
Forum: Input file
Topic: End of the Input file
Replies: 1
Views: 386

Re: End of the Input file

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.
by gmatteo
Thu Jul 02, 2020 2:43 am
Forum: Pseudopotentials and PAW datasets
Topic: Help with various Pseudopotential files read in
Replies: 1
Views: 544

Re: Help with various Pseudopotential files read in

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.
by gmatteo
Thu Jul 02, 2020 2:41 am
Forum: Post-processing Tools
Topic: Cannot locate GSR files after DOS calculations
Replies: 1
Views: 465

Re: Cannot locate GSR files after DOS 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...