Search found 257 matches

by gmatteo
Mon Sep 14, 2020 11:43 pm
Forum: Platform specific questions
Topic: Fortran runtime error
Replies: 1
Views: 204

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: 7
Views: 1012

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: 365

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: 88

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: 132

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: 110

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...
by gmatteo
Sat Jun 20, 2020 4:36 pm
Forum: Configuration
Topic: Make error 9.0.4 [SOLVED]
Replies: 4
Views: 507

Re: Make error 9.0.4 [SOLVED]

It seems the compiler is ignoring characters beyond column 132.
Can you reconfigure with:

FCFLAGS="-g -O2 --free-line-length-none"

M
by gmatteo
Fri Jun 19, 2020 5:23 am
Forum: GW
Topic: GW
Replies: 1
Views: 185

Re: GW

It's difficult to help you without the input file.
by gmatteo
Fri Jun 19, 2020 4:35 am
Forum: Input file
Topic: Using spgroup correctly
Replies: 5
Views: 291

Re: Using spgroup correctly

It is possible to use the asymmetric part of the cell (see https://docs.abinit.org/topics/SmartSymm/)
but I usually prefer to use abipy (that uses the CIF parser of pymatgen) to build the unit cell in the Abinit convention from CIF with e.g

abistruct.py convert FILE.cif
by gmatteo
Fri Jun 19, 2020 3:56 am
Forum: Input file
Topic: The use of magnetic moment, kpoints, ionmov, supercells, and DOS
Replies: 4
Views: 240

Re: The use of magnetic moment, kpoints, ionmov, supercells, and DOS

spinat with 0 0 4 on the magnetic atom positions as starting magnetic moments (I hope this is correctly understood) spinat is a [3, natom] array so you have to match the initial atomic magnetization with the atomic site as specified by xred or xcart. Note also that Abinit supports AFM symmetries as...
by gmatteo
Fri Jun 19, 2020 2:51 am
Forum: Response calculations
Topic: Electron-phonon coupling (EPC)
Replies: 2
Views: 154

Re: Electron-phonon coupling (EPC)

Also, this tutorial calculates the Eliashberg function (alpha^2F and lambda), whereas I want the matrix elements of the electron-phonon coupling g_mnv(k,q) The anaddb implementation is mainly designed for metals (conventional superconductors or transport properties in the normal metallic state with...
by gmatteo
Wed Jun 10, 2020 4:41 am
Forum: Response calculations
Topic: Phonon DOS [SOLVED]
Replies: 19
Views: 1021

Re: Phonon DOS [SOLVED]

I believe I imposed ASR. The Gamma point itself is stable, but not wavevectors near it. Here's my anaddb input file: This may be an artefact of the Fourier interpolation if the DFPT q-mesh is too coarse and/or you are dealing with tricky systems. A possibile solution (not the most elegant, I would ...
by gmatteo
Wed Jun 10, 2020 4:23 am
Forum: Input file
Topic: out of memory
Replies: 5
Views: 276

Re: out of memory

Well, it's difficult to suggest how to address the problem without looking at your input file.
I hope you are using paral_kgb = 1 with band/fft/kpoint parallelism because the default eigensolver (conjugate gradient, paral_kgb=0) can only distribute memory in k-space
by gmatteo
Mon Jun 08, 2020 9:51 am
Forum: Pseudopotentials and PAW datasets
Topic: DOJO Report and Hint explNtion
Replies: 2
Views: 174

Re: DOJO Report and Hint explNtion

it mentions that the DOJO Report and Hint explanations could be found at the end of each psp file. I looked at the end of several psp8 files from pseudodojo The doc is outdated. The hints were stored at the the end of the psp8 file in the first version of the PseudoDojo Then we decided to store the...
by gmatteo
Wed May 27, 2020 11:11 pm
Forum: Platform specific questions
Topic: Compilling Abinit 9 on mac OS [SOLVED]
Replies: 3
Views: 535

Re: Compilling Abinit 9 on mac OS [SOLVED]

Hi Gabriel, I think that with_debug_flavor="paranoid" activates compiler options to trap SIGFPE and the lhs of the condition: tsec(1tsec(1)-tcpu_last>two may trigger an exception. Can you try this patch? diff --git a/src/56_io_mpi/m_exit.F90 b/src/56_io_mpi/m_exit.F90 index c06b42018..8256cdec0 1006...
by gmatteo
Tue Feb 25, 2020 3:20 am
Forum: Input file
Topic: MIXing coefficients for ALCHemical potentials [SOLVED]
Replies: 8
Views: 510

Re: MIXing coefficients for ALCHemical potentials [SOLVED]

The code stops at the level of the parser hence it does not enter the SCF cycle. As mentioned in the error message: Found the token NPSPALCH in the input file. This name is not one of the registered input variable names (see https://www.abinit.org/doc). NPSPALCH is an internal variable (the name sta...
by gmatteo
Tue Feb 25, 2020 2:30 am
Forum: Configuration
Topic: Abinit 8.10.3 compiled with gnu 9.1: DFT calculation crash [SOLVED]
Replies: 8
Views: 1010

Re: Abinit 8.10.3 compiled with gnu 9.1: DFT calculation crash [SOLVED]

I confirm that the bug in the write statement has been fixed in Abinit9. I'd like to create a page on the yambo website with the procedure to read the WFs from the abinit code (and thus which are the needed flags for the abinit configure). I would suggest to wait for the release of Abinit9 as severa...
by gmatteo
Tue Feb 25, 2020 2:19 am
Forum: Link to other codes
Topic: Print wave-functions in NETCDF format [SOLVED]
Replies: 3
Views: 472

Re: Print wave-functions in NETCDF format [SOLVED]

Dear Davide, for the interface of abinit with yambo I need the wave-functions printed in NETCD format in abinit 8.10 To activate the output of the WFK (DEN, POT) in netcdf format, set iomode to 3 in the input file. See also the documentation: https://docs.abinit.org/variables/dev/#iomode By default,...
by gmatteo
Mon Feb 03, 2020 3:44 pm
Forum: Configuration
Topic: ABI_UNUSED failing for intel 19 with debug mode [SOLVED]
Replies: 2
Views: 325

Re: ABI_UNUSED failing for intel 19 with debug mode [SOLVED]

Hi Joe, Can I move directory "16_hideleave" to earlier in the build chain? m_xmpi is a low-level module, a tiny wrapper around the MPI library. In principle, m_xmpi should not use other Abinit modules except for basic stuff such as defs_basis and m_profiling_abi. Moving m_errors below 12_hide_mpi wi...
by gmatteo
Wed Jul 10, 2019 1:11 am
Forum: Configuration
Topic: Installing and using netcdf files for AbiPy
Replies: 1
Views: 654

Re: Installing and using netcdf files for AbiPy

What are the steps to installing netcdf programs or configuring my abinit to use/create netcdf files? Use: ./configure --with-trio-flavor="netcdf" OTHER_OPTIONS to activate the internal netcdf library. At the end of the configuration, you should see that the internal netcdf fallback has b...
by gmatteo
Tue Jun 04, 2019 4:24 pm
Forum: Configuration
Topic: Configuring with MPI [SOLVED]
Replies: 3
Views: 1122

Re: Configuring with MPI [SOLVED]

The error message given in config.log configure:23078: checking whether the Fortran Compiler supports MPI configure:23332: gfortran -o conftest -g -ffree-line-length-none conftest.F90 -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-...
by gmatteo
Tue Jun 04, 2019 12:27 pm
Forum: Post-processing Tools
Topic: How to generate a GSR file
Replies: 1
Views: 517

Re: How to generate a GSR file

The GSR is a netcdf file that is produced automatically by the code at the end of the ground-state calculation provided one has compiled Abinit with netcdf support. The easiest way to activate netcdf support consists in using ./configure --with-trio-flavor="netcdf" [OTHER_OPTIONS] when con...
by gmatteo
Fri May 31, 2019 11:15 pm
Forum: Build system
Topic: compile using 64 bits integers
Replies: 2
Views: 554

Re: compile using 64 bits integers

So, I'm not sure compiling using int64 is the solution. May be more MPI instances is the solution ? I mean, the problem may be an out of memory one ? Right, compiling with int64 is not the recommended solution. The calculation is relatively large but some dimensions scale with the number of MPI pro...
by gmatteo
Fri Nov 02, 2018 10:08 am
Forum: Configuration
Topic: compile abinit ~8.10.1 fail with gfortran 7.3.0 + openmpi3 [SOLVED]
Replies: 1
Views: 1525

Re: compile abinit ~8.10.1 fail with gfortran 7.3.0 + openmp [SOLVED]

A similar problem has been reported here

viewtopic.php?f=19&t=3935

For the time being, one has to comment that part of the code.
The issue will be solved in the next release.
by gmatteo
Tue Oct 30, 2018 6:12 pm
Forum: Configuration
Topic: Compilation fails with intel 19 compilator
Replies: 3
Views: 1141

Re: Compilation fails with intel 19 compilator

Perhaps the bug is triggered by one of the bigdft files.
Could you try to compile without bigdft to see if compilation completes successfully?