ABINIT Discussion Forums

Goto: http://www.abinit.org/documentation/helpfiles/for-v6.12/tutorial/welcome.html and check what is immediately after the INDEX. It has lines like > <a href="lesson_1.html">lesson 1<a>, lesson 2, lesson 3, lesson 4 There is apparently a stray ">". This occurs at another three l...

Thanks for the explanation. Whether it is commensurate or not will then also depend on how large size of a supercell I can choose, doesn't it? There is always a supercell (however large enough) which has the periodicity of both the original structure and the new CDW structure.....right? In case I ca...

Thank you for your reply. I have done an example calculation here: http://skku.homeip.net/lahaye/abinit/NumberOfElectrons/ which hopefully demonstrates my issue. This is NaTaO3, but I use 8 unit cells in my supercell and replace one oxygen atom a by C atom, to simulate a kind of doping effect. Hence...

Hi, I'm asked to calculate Charge Density Waves (CDW) with Abinit. I kind of understand the very basics of this phenomenon: in conductors a small rearrangement of the ions will lower the total energy by creating a small bandgap at the fermi energy. Can somebody help me find the important parameters ...

Hi, My PC has an Intel Core i7 CPU 950 @ 3.07GHz. I use abinit 6.2.3 on an up-to-date Fedora system with openmpi 1.4.1 I have configured and compiled as follows: $ ./configure --prefix=/opt/abinit --program-suffix="_openmpi" \ --disable-netcdf --disable-bigdft --disable-wannier90 --disable...

Hi, Abinit 6.2.3 runs on a up-to-date Fedora system (32 bits and with kernel 2.6.32-PAE). The system has 6 GB RAM and 12 GB swap. When I run the abinit job, it terminates because it cannot allocate 2779.477 Mb (see below for snippet from the log file). How come this job cannot find 2779.477 MB (= 2....

Hi, Abinit 6.2.3 runs on a up-to-date Fedora system (32 bits and with kernel 2.6.32-PAE). The system has 6 GB RAM and 12 GB swap. When I run the abinit job, it terminates because it cannot allocate 2779.477 Mb (see below for snippet from the log file). How come this job cannot find 2779.477 MB (= 2....

Check:

http://www.abinit.org/documentation/helpfiles/for-v6.2/input_variables/vargs.html#chkprim

The next item chksymbreak is wrongly glued to the end of chkprim.

Please fix.
Rob.

I wonder if following could do what you want: optcell 9 ionmov 0 acell A1 A2 A3 rprim sqrt(3/4) -0.5 0.0 sqrt(3/4) 0.5 0.0 0 0 1.0 xred 0.0 0.0 0.0 1/3 1/3 0.0 where A1 = A2 and should be some reasonable values for the graphene sheet. Then A3 should be large, to neglect interactions between layers. ...

I think you should use the proper optcell parameter, e.g. opcell = 9 leaves the
third lattice vector unchanged, while optimizing the first two.

Rob.

Hello, I'm using abinit 6.2.3. I have a problem with the integrated density of states in the DOS output file (prtdos 2). The top of the DOS output file gives the fermi energy, but the integrated DOS value at that fermi energy is not equal to the total number of electrons in the cell. I have been usi...

Hi, I am doing a density of states and bandstructure calculation of graphene, graphite, and related structures. When I have the DOS and bandstructure graphs, I wonder which lines/peaks belong to pi-orbitals (perpendicular to the carbon plane) and sigma orbitals (in-plane of the carbons). Is it possi...

Hi Ham, I believe there's not much vizualization software that can import Abinit in/output files directly. My choice for vizualization is VMD (m) which can handle easily 'home-made' plugins to convert alien formats into its own. I have written a plugin to read Abinit output files (GEO, DEN) into VMD...

Although LDFLAGS="-static" worked for 6.0.4, it does not anymore for 6.2.1.
Instead use FC_LDFLAGS="-static".

R.

Hi, I had the configure options set up for creating a static executable with version 6.0.3 (and I've double checked that they still work now), but the same configure options do not create a static executable with 6.2.1. See also my last posting to this thread: http://forum.abinit.org/viewtopic.php?f...

Hi,

This does not seem to work anymore with 6.2.1.

I use the same configure options, but with 6.2.1 it produces
the usual dynamically linked abinit executable.

Has the procedure changed from 6.0.3 to 6.2.1 ?

Thanks,
Rob.

Hi, On my system often there are several instances running of abinit. Occasionally I have to kill one of those abinits running. It is then difficult to find out which process id (PID) I should kill. If the STATUS file would also show the PID of the running abinit, that would make life much easier. I...

Hi, When I run abinit, I have this comment in the log file: --------------------------------------------------------------------- getcut : COMMENT - Note that boxcut > 2.2 ; recall that boxcut=Gcut(box)/Gcut(sphere) = 2 is sufficient for exact treatment of convolution. Such a large boxcut is a waste...

Hi,

When a job is abruptly terminated in the middle of a calculation,
a foobar_STATUS is left behind.

Can I use this STATUS file to easily restart the calculation
more-or-less from the place where it was stopped?

If yes, then how can I do that?
Is this documented somewhere?

Thank you!

Rob.

I've been given another hint via the developper's forum.

It seems to be possible to link external software with the abinit parser
code so that the software can read input files with the same flexibility.

I have to figure out how it has to be done, but that should solve my problem too.

Rob.

Of course one can create some kind of rediculous input file with silly criteria so that the executable effectively doesn't calculate anything and just prints out the coordinates of the atoms in a GEO file. But that solution I'd like to avoid. Instead it would be great if there's an input parameter t...

Hi, I need an easy and quick method to only convert an abinit input file to a standard output file (e.g. XYZ-format), which can be read easily by graphical software. This allows me to verify the atoms' coordinates before starting a DFT calculation. I am using VMD as my graphical toolkit. It cannot r...

Hi, I need an easy and quick method to only convert an abinit input file to a standard output file (e.g. XYZ-format), which can be read easily by graphical software. This allows me to verify the atoms' coordinates before starting a DFT calculation. I am using VMD as my graphical toolkit. It cannot r...

Thank you!
That solved the problem.

R.

You must redirect the input file and (optionally) redirect the output to a log file.
For example: abinit < t11.in > logfile

Read the beginning of the tutorial!

R.