#

FAQ

This document provide answers to very basic questions about ABINIT, as well as to more elaborate questions. We have taken the DACAPO FAQ pages as a model.

##### Copyright (C) 2003-2009 ABINIT group (MMikami, JMBeuken, XGonze)
This file is distributed under the terms of the GNU General Public License, see ~ABINIT/Infos/copyright or http://www.gnu.org/copyleft/gpl.txt .
For the initials of contributors, see ~ABINIT/Infos/contributors .

## Summary

- General

- What is ABINIT ?
- What can ABINIT do ?
- What cannot ABINIT do ?
- Does it run in parallel ?
- Is there a summary about ABINIT ?
- Is there a review paper on ABINIT ?
- What is the copyright conditions ?
- I like to contribute the ABINIT project in any way. How ?
- I like to add my subroutine to ABINIT. How ?
- Is there a graphical user interface (GUI) ?
- Is there a mailing list (ML) ?
- I think there is a bug - making a bug report
- I didn't receive any response to my question on ML. Why ?
- Is there a tutorial ?
- Is there a good pseudopotential database ?
- Are there (Vanderbilt-type) Ultrasoft pseudopotentials in ABINIT ?
- How do I generate a new pseudopotential ?
- Recent studies based on ABINIT ?
- I am a complete newbie. How do I get started ?
- The documents seem too many for a newbie like me to read through. How to find relevant documents for my questions ?
- I am new to Density Functional Theory/Pseudopotential+Planewave: What should I know ?
- Why do my ABINIT results differ from experimental results ?
- (to be added, if any)

- Installation of ABINIT
  - What hardware/software do I need ? How to install ?
  - How to update ? How to catch up the latest versions ?
  - I find errors during compilation. How should I do ?
  - Is my installation successful ?
  - I cannot make "abinip". What should I check ?
  - Linux_cpp_P6 : /lib/cpp failed to remove some C style comments
  - Linux_cpp_Alpha : /lib/cpp failed to remove some C style comments
  - Linux_Intel : problem to run abinit with dynamic IP allocation
  - Win2K_Intel : How to install ABINIT on Windows2000 with PGI ?
  - Linux_Intel : compiler versions and options for IFC
  - MacOSX_Absoft: buffer allocation failed
  - IBM SP : Memory allocation error
  - (to be added, if any)
- Setting up calculations

- How can I quickly setup a calculation for my model ?
- Is there anybody willing to give me an input file example?
- How to find test cases relevant to my target system ?
- Is there a rule of thumb for parameter settings ?
- How should I choose the key calculation parameters ?
- (to be added, if any)

- Tips to use ABINIT
  - How to choose the q-points ?
  - How to set "sciss" with other parameters ?
  - Compaq-Digital Tru64 Unix : "forrtl: error (65): floating invalid" in non-SCF cycles.
  - Negative frequencies in phonon band structure
  - Non-zero phonon frequencies at Gamma point ?
  - ASR: large changes in phonon frequency
  - Alchemical mixing of PSPs
  - Slab calculation
  - GW calculation
  - Spin-orbit coupling
  - Berry phase
  - Bader charge analysis
  - FHI98PP + core correction
  - Restarting calculation
  - nbands for metallic case
  - scfcge: ERROR - Potential-based CG line minimization not converged
  - How to prepare input data for my crystal ?
  - energy selective charge density
  - Bandstructure: why my output includes fewer k-points than I expected ?
  - Geometry constraints for selected atoms in geometry optimization/Molecular Dynamics
  - cut3d: Atomic Sphere Analysis of a wavefunction for selected kpt/band
  - Piezoelectric calculation
  - Geometry optimization Under Pressure
  - (to be added, if any)
- Parallelisation of ABINIT
  - SGI Origin 2000 : speed-up problem
  - parallelization over bands in ABINIT
  - (to be added.if any)
- Utilities

- kptgen : accuracy of atomic positions

- Misc. trouble shooting

- Reading old WF/DEN/POT files with v3.4 (and later versions)
- Error in reading my input file
- Fermi energy is not printed out ?
- Negative value of DOS ?
- Tetrahedron method
- PAW method
- unit of oscillator strengths ?
- latest definition of Bohr in Angstrom
- What is IFC ?
- I cannot download a file "foo" from "ftp.abinit.org/pub/incoming". Why ?
- Why are different symmetries assigned by different versions of ABINIT ?
- Why do ABINIT and other calculation methods produce different results ?
- (to be added, if any)

- What is ABINIT ?
Please refer to the top page.

- What can ABINIT do ?
Please refer to the document "Features" in the top page or ~ABINIT/Infos/Features/features_*.html.

- What cannot ABINIT do ?
Too many things to describe ! What is not described in the documents such as "Features" may be unavailable in the present ABINIT.
If you find what ABINIT cannot do at present and want to implement it, you are welcome to contribute to the ABINIT project ! (ABINIT is an open source project that favors development and collaboration)
You may subscribe (or unsubscribe) "Developer" Mailing list (develper@abinit.org).

- Does it run in parallel ?
Yes, please refer to the document "Features" ("B. Speed in the parallel version") for detail. Then, examine the document ~ABINIT/Infos/paral_use .

- Is there a summary about ABINIT ?
Yes, please download the pdf file from the top page: "ABINIT : a project that favors development and collaboration (short presentation of the ABINIT project - 10 pages in pdf)"
See also "Features" (~ABINIT/Infos/Release_notes/release_notes_*.html).
NB: for Japanese users: ABINIT is briefly introduced in "Kotai-Butsuri" (Solid State Physics), vol.38, No.3, p.219 (2003) by M. Mikami.

- Is there a review paper on ABINIT ?
"First-principles computation of material properties: the ABINIT software project",
X. Gonze, J.-M. Beuken, R. Caracas, F. Detraux, M. Fuchs, G.-M. Rignanese, L. Sindic, M. Verstraete, G. Zerah, F. Jollet, M. Torrent, A. Roy, M. Mikami,Ph. Ghosez, J.-Y. Raty, D.C. Allan.
Computational Materials Science 25, 478-492 (2002).
Citation of this paper in your publications would be highly appreciated. Please refer to "Acknowledgements"(~ABINIT/Infos/acknowledgments.html).

- What is the copyright conditions ?
ABINIT software (version 3 and later) are distributed under the very liberal GNU General Public License.

- I like to contribute the ABINIT project in any way. How ?
There are many ways to help the ABINIT project, including sponsoring.

- I like to add my subroutine to ABINIT. How ?
Just add it to object_list in the Src_* directory in which you place the subroutine.
If you are considering submitting your new routine to be included in an upcoming Abinit release, you should read the documents in Infos/Notes_for_coding. It is probably a good idea to follow these rules even if you only intend the routine for your own use, since it will probably help eliminate bugs.
(cited from Dr. Hamann's post)

- Is there a graphical user interface (GUI) ?
Some softwares may be helpful to check geometries of your models or visualize contour maps/isosurfaces of your charge densities etc.

- VASP Data Viewer
- Scilab (free MATLAB lookalike for linux)
- XCrysDen
- OpenDX : see also for examples
- Jmol
- VENUS
- XtalEdit
- MOLDEN (see also the FAQ for molecular crystalline systems)
- Mercury (e.g. check contacts, H-bonds, powder X-ray patterns)
- (to be completed...)

- Is there a mailing list (ML) ?
There are presently four ABINIT mailing lists :

- Announce List (announce_@_abinit.org - Announce of new ABINIT release, urgent bug reports, etc.)
- Forum List (forum_@_abinit.org - The ABINIT Users Mailing List)
- Advisory Committee List (advisory_@_abinit.org - The ABINIT Advisory Committee Mailing List)
- Developer List (developer_@_abinit.org - The ABINIT Developer Mailing List)

Access to the mailing list manager, in order to subscribe, unsubscribe, get the e-mail addresses of the list, access the archives. (Keyword search in the archives is available.) We appreciate very much your consideration for our Netiquette to keep our MLs most effective.

- I think there is a bug - making a bug report
Thank you ! Please read this (or ~ABINIT/Infos/problem_report) before submitting your bug report.

- I didn't receive any responses to my question on ML. Why ?
Well, there might be some reasons:

- It might be a FAQ. Please check this FAQ list carefully.
- Answers might be already available somewhere in ~ABINIT/Infos/*. Please try
  grep -i (keyword for your question) *
  at the directory, and the directries therein. ("grep -ri" will help for recursive search)
- Answers might be already available in the forum archive. Please try keyword search there.
- Your question might be unclear with insufficient disclose of your case.(Readers cannot guess what you are doing !) Otherwise, your mail might be too lengthy/winding. Please write specific/concise e-mail for readers to follow. Attachment of input/output could help.
- Your question might be too tough to respond quickly. Otherwise, those who have answers have less time to reply at that time, unfortunately. Please be patient ...
- Your question would be beyond our interest. Please ask at other sites.
- Other possibilities...
  (e.g. Your question might suggest that you give up efforts to learn ABINIT.)

You may remember, "Nobody is paid to give a service to the ABINIT community."
If you need so-called "user-support" at any cost, it might be a good idea to buy a commercial package (with full user-support). Yet you can have more chances to get responces, if your question can attract readers' attentions.

- Is there a tutorial ?
Yes, follow this.
You can find them in ~ABINIT/Tutorial/ in the tar.gz ball. Please read the README file in it. New Abinitioners are encouraged to try them.

- Is there a good pseudopotential database ?
You may find pseudopotentials from the top page :
LDA pseudopotential files :

- Troullier-Martins pseudopotentials for most of the elements in the periodic table, generated by A. Khein and D.C. Allan
- Goedecker-Teter-Hutter pseudopotentials for selected elements
- Hartwigsen-Goedecker-Hutter pseudopotentials for most of the elements in the peri odic table.
- Teter "extended norm-conserving" pseudopotentials for selected elements
- Fritz-Haber-Institute (FHI) pseudopotentials for selected elements (Troullier-Martins scheme)
- LDA core-hole pseudopotential files for selected elements

GGA (PBE) pseudopotential files :

- Fritz-Haber-Institute (FHI) pseudopotentials for selected elements (Troullier-Martins scheme)
- Hartwigsen-Goedecker-Hutter pseudopotentials for selected elements

The formats for the pseudopotential are described in the documents in ~ABINIT/Infos/Psp_infos/.
But please remember, "Use at own risk !" Pseudopotentials should always be tested in well-known situations, before using them for predictions ...
Specifically, transition metals should be carefully checked.(See, for example, ~ABINIT/Infos/Psp_infos/psp1.data)

- How do I generate a new pseudopotential ?
Hereafter we assume that you have expertise in pseudopotentials:
For Fritz-Haber-Institute (FHI) pseudopotentials, you can use FHI98PP package. Please read ~ABINIT/Psps/Psp_infos/psp6.info. See also the e-mail for references helpful in making good pseudopotentials.
You may use OPIUM package for "Optimized pseudopotentials" developed by A. M. Rappe et al.
Other PP packages might be available. (If so, please let us know.)

- Are there (Vanderbilt-type) Ultrasoft pseudopotentials in ABINIT ?
No. But projected augmented wavefunction method (PAW) is now under development (from version 4), so speed-up may be expected.

- Recent studies based on ABINIT ?
Please look into ABINIT bibliographical database: registration and list of papers that acknowledge ABINIT.

- I am a complete newbie. How do I get started ?
A recommendation would be :

1. Read this (~ABINIT/Infos/welcome.html")
2. Read installation_notes (~ABINIT/Infos/Installation_notes/install_*.html).
3. During installation, read "New user guide" (~ABINIT/Infos/new_user_guide.html).
4. Then try Tutorials (~ABINIT/Infos/Tutorial/welcome.html), consulting help_files (Abinis (main), Abinis (respfn), Mrgddb,Anaddb,AIM (Bader)) and "List of input variables" (~ABINIT/Infos/keyhr.html) when needed.
5. Then try Test_*. (See "README" file to know how to run the tests) Please be aware that some input parameters are deliberately reduced for short CPU time.
6. Then go into the ~ABINIT/Infos directory. Read memos, references cited in bibliography, ... etc.

- The documents seem too many for a newbie like me to read through. How to find relevant documents for my questions ?
Try
grep -i "keyword related to your question" *
grep -ir "keyword related to your question" * # NB: "-r" for recursive search
find . -name \* -print | xargs grep "keyword related to your question"
at ~ABINIT and directories therein (esp. ~ABINIT/Infos/* and ~ABINIT/Test_*/).

- I am new to Density Functional Theory/Pseudopotential+Planewave: What should I know ?
You should indeed learn theoretical background to make the most use of ABINIT code.
We recommend the book by Richard M. Martin (published in Summer 2004), Cambridge University Press.
Electronic Structure : Basic Theory and Practical Methods (ISBN: 0521782856)
For details, see http://www.cambridge.org/uk/catalogue/catalogue.asp?isbn=0521782856

You can also consult :
M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulos, Rev. Mod. Phys. 64, 1045-1097 (1992), and references therein.
For the pseudopotential technique,
M. Fuchs and M. Scheffler, "Ab initio pseudopotentials for electronic structure calculations of poly-atomic systems using density-functional theory," Comput. Phys. Commun. 119, 67-98 (1999), and references therein.
You can also consult references cited in the ABINIT bibliography (~ABINIT/Infos/bibliography.html) as well as the book G.P.Srivastava, "Theoretical Modelling of Semiconductor Surfaces"(World Scientific, 1999), or examine links from ElectronicStructure.org
You can remember,"There is no royal road to knowledge (learning)" or "The more haste, the less speed." Good continuation !

- Why do my ABINIT results differ from experimental results ?
Many reasons !
Your input (system/assumption, input parameters, pseudopotentials ...) might be wrong;
ABINIT might have bugs;
the present formalism in DFT (LDA, GGA, etc.) could not treat your case well ...
So you may post your question to the "Forum" mailing list (forum_@_abinit.org).
Please describe specific/consise information as possible in your e-mail. Attachment of your (full) input file along with your ABINIT version will be fine to avoid guessing what you are doing with ABINIT.
Your output/log file will also help us to diagnose your case.(Please be aware that the size of your output/log should be moderate for posting.)
You might want to follow some threads in the Forum archive to know that it is not always straightforward to obtain plausible results :
"PP for Ga with 3d as valence"(read also the follow-ups)
"Cu and Au bulk modulus"(read also the follow-ups)
"short lattice constant of Ni within LDA"
"NaCl bulk modulus"
"acoustic phonons in metals (alkali/earth-alkali compounds)" (follow also the hyperlinks)
"LDA overbinding and TM pseudopotentials" (read also the follow-ups)

- What hardware/software do I need ? How to install ?
See "Installation notes" (~ABINIT/Infos/Installation_notes/install_*.html).

- How to update ? How to catch up the latest versions ?
You can download the latest versions from the ABINIT web page. The version changes and urgent bug reports are announced on the ABINIT "announce" Mailing List (announce_@_abinit.org).
So you are welcome to subscribe (or unsubscribe).
You can check the major difference between the latest version and the prior version from "Release_notes"
(~ABINIT/Infos*/Release_notes/release_notes_v*.html)

- I find errors during compilation. How should I do ?
If you think that you find a compiler error, please report it following instructions in "problem_report"
(~ABINIT/Infos/problem_report) before submitting your bug report.

- Is my installation successful ?
Please try Test_* jobs and check "fldiff.report" files.
You might need to check diff.* also, if fldiff.report does not give sufficient information. If your result appears weird, please check "known_problems"(~ABINIT/Infos/known_problems.*) to see if your case is reported.

- I cannot make "abinip". What should I check ?
The "makefile_macros" file for "abinip" may be different from that for "abinis." Please check other makefile_macros in ~ABINIT/Machine_dept_files/"Your platform"/.

- ABINIT_Linux_cpp_P6 : /lib/cpp failed to remove some C style comments (22 Feb 1999)

> On an Intel P6 running Linux, I found that /lib/cpp failed to remove some C style comments, thus making compilation of abinis.f impossible.
> By using a different version of cpp (/usr/lib/gcc-lib/i386-redhat linux/2.7.2.3/cpp)
> I managed to get around this problem.

> +----------------------------------------------------+
> Andrew Horsfield e-mail: horsfield@fecit.co.uk
> FECIT, 2 Longwalk Road, Stockley Park, Uxbridge,
> Middlesex UB11 1AB, United Kingdom.
> phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422
> +----------------------------------------------------+

- ABINIT_Linux_cpp_Alpha : /lib/cpp failed to remove some C style comments (22 Feb 1999)

> (From Vitaliy Godlevsky, 2 March 2000)

> Summary: Installation of Abinit under Alpha LINUX (Red Hat)

> (Hardware : Dual Alpha DEC 21264 500 MHz system)
> While compiling abinit by Compaq Fortran compiler "fort" I used Linux CPP (/lib/cpp).
> There was a problem with C style comments (/* */) that weren't removed from the code. Using CPP without -C option resulted in removing C++ style comments ( // ). This, in turn, messed up input subroutines which rely on fortran90 string operations //
> The solution was to use C preprocessor provided by fort which is invoked with "fort -P".
> Since fort -P file.f write the preprocessed file in file.i, I had to modify some makemake scripts changing the part concerning CPP command by something like:

> abinis.o: abinit.f

> > \$(CPP) \$(CPP_OPTS) \$(CPP_FLAGS) abinit.f
> > \$(FC) \$(MAIN_ROUTINE_FFLAGS) \$(FFLAGS) -c abinit.i
> > mv abinit.o abinis.o
> > rm -f abinit.i

> PS : see the file Machine_dept_files/DEC/makefile_macros.DecLinux

- ABINIT_Linux_Intel : problem to run abinit with dynamic IP allocation

> I modified /etc/hosts to include:

> > 127.0.0.1 dmt.ipm.virginia.edu dmt

> I used the loopback IP as my machine has never been IP'd due to dynamic IP allocation.
> So, after adding dmt to the /etc/hosts file, abinis appears to run.
> Also, there's the ability to set the environmental variable PGHPF_HOST.
> i.e.

> > set PGHPF_HOST dmt

> or

> > setenv PGHPF_HOST dmt

> +----------------------------------------------------+
> Dave Tater
> teter@virginia.edu
> +----------------------------------------------------+

- Win2K_Intel : How to install ABINIT on Windows2000 with PGI ?

>     Answer by Luc Sindic:
>              First, you need to have a minimal knowledge of Unix systems
>     because PGI Workstation is a "Bash" unix shell under Windows. Read the
>     "PGI Workstation documentation" and record the differences with a DOS prompt
>     window (e.g. / for \ ; cp for copy ; ls for dir, ...)
>              If this is not already done, you have to "unpack" the Abinit
>     package under PGI Workstation, in a clean subdirectory called ABINIT_HOME below,
>     with the following commands:
>                      gunzip src_test_3.3.3.tar.gz
>                      tar xvf src_test_3.3.3.tar

>              Then, browse the file
>                      ABINIT_HOME\Infos\Installation_notes\install_v3.3.htm
>     You will see how to make the executables. You will also see that you need
>     to have Perl installed on your PC and how to get it if necessary.
>              Before making the executables, you have to customize your
>     "makefile_macros" file that describes the compilers paths, options, ...
>     You can derive it from the one I'm using on my PC:
>        ABINIT_HOME\Machine_dept_files\Intel_P6\makefile_macros.PGIwk.3.0

- Linux_Intel : compiler versions and options for IFC (Intel Fortran Compiler)
The versions/options of your Intel compiler appear crucial to compile the source package nicely. See, for example, e-mail#1,#2,#3,#4,#5.
Please check carefully the archives in the "forum" mailing list to know the latest information.(Try keyword search)
If your IFC does not work, it may be a good idea to try other version of IFC. The older versions of IFC (and MKL) can be found from this FTP site (and this FTP site). The license files you get sent from the Intel can work with the older versions of the compiler and MKL.

- MacOSX: Buffer allocation failed
MacOSX users might encounter the following message :
*** malloc_zone_malloc[1081]: argument too large: -678934464
? FORTRAN Runtime Error
? Buffer allocation failed
It may depends on versions of OSX and Absoft Fortran.
To avoid this error, a dummy input sentence may be effective in driver.f. Around line 170-190 (just before allocate sentences),
------------------------------
(snip)
!DEBUG ! Do not comment this line for the time being XG020913
write(6,*)' driver : before allocate, npsp= ',npsp
!ENDDEBUG
i_dummy = 0 !! may be inserted for MacOSX
!Allocation of some arrays independent of the dataset
allocate(psps%filpsp(npsp))
(snip)
------------------------------

- IBM SP: Memory allocation error
Read this e-mail (and the follow-ups).

- How can I quickly set up a calculation for my model ?
- Is there anybody willing to give me an input file example ?
First, you are strongly recommended to read the "New Users Guide" (~ABINIT/Infos/new_user_guide.html) and try Tutorials, before you case is set up.
Then, you can find input files in Tutorials and Test_* similar with your case, and use them as template. (Please read "README" files, then you will find ...)
Please be aware that parameters relevant for convergence (energy cutoff, k-points, nstep, ntime, etc.) should be carefully checked for physically/chemically meaningful results.

- How to find test cases relevant to my target system ?
Try
grep -i "keyword related to your question" *
at ~ABINIT/Test_* and ~ABINIT/Tutorial.
Relevant keywords (input variables) can be found in "List of input variables"(~ABINIT/Infos/keyhr.html).
Kindly remember that you are encouraged to run through all the Test_*/Tutorial first.

- Is there a rule of thumb for parameter settings ?
- How should I choose the key calculation parameters ?
You can learn how to set parameter settings in Tutorials.
(More specific ? e.g., larger cutoff will be necessary for 2nd-rows elements (C,N,O,F...), 3d-transition metal elements, 4f rare-earth elements, ...)

- Parallelisation_SGI : Speed_Up problem

> Doug Ritchie wrote:

> > I have a question.
> > I did a parallel run (on a SGI Origin 2000) on the simple test case of an energy
> > band calculation on Si with input file starting as:
> >
> > # Si in diamond structure; 60 special points in core; low ecut.
> >
> > acell 3*10.26311
> > densty 1.2
> > diemac 12.0d0
> > ecut 5.8
> > mkmem 60
> > natom 2 nband 4
> > ngfft 3*16
> > nkpt 60
> > nline 3
> > nstep 15
> > nsym 24
> > ntype 1
> > rprim 0 .5 .5 .5 0 .5 .5 .5 0
> > symrel
> > ...
> >
> > This runs very quickly and the times are:
> >

> np | t(0) | sum(t(p))
> 1 | 101.4 | 101.4
> 2 | 52.9 | 105.7
> 3 | 37.8 | 113.5
> 4 | 30.0 | 120.2
> 5 | 25.4 | 127.2
> 6 | 22.1 | 132.1
> 10 | 15.7 | 157.2
> 12 | 14.2 | 170.8
> 15 | 12.7 | 189.8
> 20 | 11.2 | 224.1
> 30 | 9.8 | 296.3

> > which isn't great, I am wondering if I am doing something obviously silly.
> > I did take np to be an integral divisor of nkpt = 60
> >
> Xavier Gonze wrote:
> I think that you are doing the right things. Simply, the test case is not
> suited for as many processors. I have to mention a few things :

> - the parallelisation is only done over the k-points, and in abinip
>   there are some sequential steps that last together a few seconds (4-6 secs) before and after the k-point loops.
> - in this test case, for each k point, the computation inside the k-point loop
>   is on the order of 1-2 seconds. This test case has been chosen to run fast,
>   while still sufficiently efficient for 4 and 10 processors
> - this k-point parallelisation needs very few communication, and that is why it
>   is called 'efficient'. It works well even on a cluster of workstations linked
>   by Ethernet 100 Mb/s...

> So, what you observe is the influence of the sequential part,
> and there is nothing to do without modifying the test case, I think.

> - a better speed-up is obtained when systems with higher cut-off energy (ecut)
>   and number of bands are treated. These usually take much more time, and the
>   ratio between the sequential part of the code to the parallel part of the
>   code decreases. But except for some metallic systems,
>   one needs fewer k point (between 1 and 10 let's say) in realistic situations.
> - in order to obtain an artificially better speed-up, you can for example change ecut,
>   and instead of ecut 5.8 , use ecut 20 (unrealistic for Si, but allright for tests),
>   and also instead of nband 4 , use nband 8.
>   By these operations, the time needed per k-point will be multiplied by about 16.
>   The time of some sequential parts will also change, but the behaviour should already be better...

> +----------------------------------------------------+
> Doug Ritchie
> ritchie@neon.sao.nrc.ca
> +----------------------------------------------------+

- parallelization over bands in ABINIT
See, for example, this.

- Utilities_kptgen : accuracy of atomic positions

> When I used KPTGEN today (May 27, 1999), I had a curious experience.
> (In fact, no curious... Only I might have not realized the following.)

> If I use the following input for "kptgen", it fails.

> Example unit cell

> 7.1431642 7.1431642 12.402272 acell
> 0.8660254037844386 0.5 0 -0.8660254037844386 0.5 0 0 0 1 rprim
> 5 3 natom, ntype
> 1 2 2 3 3
> 0.00000 0.00000 0.00000
> 0.33333 0.66667 0.29000
> 0.66667 0.33333 0.71000
> 0.33333 0.66667 0.64000
> 0.66667 0.33333 0.36000
> 0 0 ibrav, inpgd
> 0 nkpt
> 4 4 4 0 0 0 Monkhorst-Pack indices and origin for grid

> The error message in standard output is as follows:

> > cpointg error: atom 2 doesn't fit symmetry 2
> > rotated coord -2.062033266329 -3.571617815821 3.596658880000
> > other atom 2.062095127946 3.571582100000 8.805613120000
> > difference -4.124128394275 -7.143199915821 -5.208954240000
> > phases -.500036275549 -.499981861897 -.876306680044
> > rotation matrix: -.50 -.87 .00 .87 -.50 .00 .00 .00 1.00
> > nonsymmorphic transl: .000000000000 .000000000000 .000000000000

> But If I use the following input (the digits of "xred" are increased),
> it did work !

> Example unit cell

> 7.1431642 7.1431642 12.402272 acell
> 0.8660254037844386 0.5 0 -0.8660254037844386 0.5 0 0 0 1 rprim
> 5 3 natom, ntype
> 1 2 2 3 3
> 0.000000000 0.000000000 0.000000000
> 0.333333333 0.666666667 0.290000000
> 0.666666667 0.333333333 0.710000000
> 0.333333333 0.666666667 0.640000000
> 0.666666667 0.333333333 0.360000000
> 0 0 ibrav, inpgd
> 0 nkpt
> 4 4 4 0 0 0 Monkhorst-Pack indices and origin for grid

> Thus I really realized that the digits of "xred" is very important and that enough digits of "xred" are prepared in all the input examples
> (in.*). (The criterion condition (the parameter of "tolerance") in cpointg.f seems to be set severely.)

> +-------------------------------+
> Masayoshi Mikami
> Mitsubishi Chemical Corporation (Research and Development Division, Yokohama Research Center)
> Phone: +81-45-963-3265 Fax:+81-45-963-3947
> E-mail: mmikami@rc.m-kagaku.co.jp (office), mmikami@yk.rim.or.jp (home)
> +-------------------------------+

- Tips to use ABINIT : How to choose the q-points ?

> (From Patrick Tepesh, on 13/9/1999)
> Can you give me some hints or refer me to a paper to help me choose q-points for integrating to obtain free energies?
> My first impulse is to just use the same MP grids as for the electronic structure calculations,
> but it seems from looking at a few papers that this might not be the way most people do it (the papers I've seen so far do not give much detail about the choice of the grid).

> (From Masayoshi Mikami, on 27/9/1999)
> Which is the smartest way to choose the q-points for finer mesh in Hexagonal (or Trigonal) Lattice case ? (Is it the same way in the choice of "kpt" in SCF-calculation (MP-mesh)?)

> (Response)
> About the q-points : usually, one needs in any case the gamma point (for effective charges and dielectric constant).
> This point is not part of the usual Monkhorst-Pack (shifted) grids. Unlike with the k-points for the electronic structure calculations,
> the workload of each q-point can be very different : if there are remaining symmetries, they can be used fully : the code automatically select the "primitive" perturbations, and do not care about their symmetric. The code even decreases the number of k points if there is still some residual symmetry to be taken into account for one perturbation. Even if unshifted MP grids usually lead to more q-points than shifted grids, each of these q point may be more symmetric, and thus much faster to compute.
> The current attitude (see the work in Ferroelectrics 206-207, pp. 205-217 (1998), especially p. 207) is to use a set of MP grids who share common q-points, so that one can judge of the convergence by simple "data reuse"...

- Tips to use ABINIT : How to set "sciss" with other parameters ?

> (From Masayoshi Mikami, 27/9/1999)
> How to set "sciss" with other parameters (or dataset) ...
> I tried another input, just adding "sciss4 0.0735294117647" in the input below. (The calculated band gap is smaller than experimental one by about 2 eV. Thus the above "sciss4" corresponds to 2 eV.) It affected phonon-frequencies as well as Born effective charges and dielectric tensors... Is this really expected ?! We should not set both "rfphon 1" and "rfelfd 1" at the same time when non-zero "sciss" is applied ?

> (Response)
> When a non-zero "sciss" is applied, all the response functions are affected. So, the reaction of the code is normal. On the other hand, within the present understanding of the scissor approximation, in order to get physical results, the scissor should only be applied to the dielectric tensor calculation (with rfelfd 1). So, it is right that rfphon 1 and rfelfd 1 calculations should be done separately when a scissor is used.

- Tips to use ABINIT : Compaq-Digital Tru64 Unix : "forrtl: error (65): floating invalid" in non-SCF cycles.

> (From Fabio Finocchi, 6 Nov 2000)
> This FAQ is addressed to the owners of Compaq-Digital Tru64 Unix workstations on which the sequential version abinis runs. On these machines, a bug was noted at the very beginning of the non-SCF cycles, just after the calculation of the band residuals, resulting in a message like this:
> " forrtl: error (65): floating invalid "

> After some tests, I noted that - for a given system - this happened when increasing the number of bands, rather independently of

> 1. their occupancy
> 2. the number of k-points
> 3. the number of G-vectors.

> Thus, I guessed that the bug should concern the linear algebra routines (BLAS) used for the calculation of band residuals. Indeed, the latters turned out to be wrong, through a comparison with the runs carried out on another machine. Rather than looking into the code, I tried to link with the BLAS routines supplied with the ABINIT package, by explicitly modifying the machine dependent makefile. This action fixed the bug, on Tru64-ev6 as well as on Tru64-ev56 systems (that is, for two distinct processors but using the same operating system). The modification in the makefile_macros file is below.
> If anybody is aware of other less empirical remedies to the same bug, or if someone noted other bugs linked to the use of the BLAS library provided with the Compaq Tru64-Unix workstations, please let me know.

>     # Definition of libraries
>         #BLAS_A=-ldxml
>         BLAS= Lib_blas
>         BLAS_A= $(BLAS)/blas.a -ldxml
>         LIBS= $(LAPACK_A) $(FFTS_A) $(NUMRECIP_A) $(BLAS_A)

> Fabio Finocchi

- Tips to use ABINIT : Non-zero phonon frequencies at Gamma point ?
Read this summary. If you have interesting test results based on Doug's idea, please let us know. (Thank you in advance !)

- Tips to use ABINIT : ASR: large changes in phonon frequency
Read this.

- Tips to use ABINIT : Alchemical mixing of PSPs
To know implementation in ABINIT, read this.
See also: "First-principles study of lattice instabilities in Ba_{x}Sr_{1-x}TiO_3"
Ph. Ghosez, D. Desquesnes, X. Gonze and K. M. Rabe, AIP Conf. Proc. 535, 102-110 (2000).
See also for another Alchemical mixing.

- Tips to use ABINIT : Slab calculation
See, for example, e-mail#1,#2(and the hyperlinks therein).

- Tips to use ABINIT : GW calculation
Why does the presence of non-symmorphic operations in the symmetries list cause problems ? etc.
Read e-mail#1,#2,#3, and #4.

- Tips to use ABINIT : Spin-orbit coupling
See, for example, this.

- Tips to use ABINIT : Berry phase
See, for example, this.

- Tips to use ABINIT : Bader charge analysis
See, for example, this.

- Tips to use ABINIT : FHI98PP + core correction
Please read ~ABINIT/Psps/Psp_infos/psp6.info. See also, e-mail#1,#2.

- Tips to use ABINIT : Restarting calculations
It might be a good practice to have *DEN, *WFK etc. for restart
(keyword: prtden, prtwf).
If you run structure optimizations/molecular dynamics,
you might want to reserve geometries at each step (keyword: prtgeo).

- Tips to use ABINIT : nbands for metallic case
See, for example, this.

- Tips to use ABINIT : scfcge : ERROR - Potential-based CG line minimization not converged
See, for example, e-mail#1,#2.

- Tips to use ABINIT : fconv : WARNING - ntime=xxx was not enough Broyd/MD steps to converge gradients:
See, for example, e-mail#1,#2.

- Tips to use ABINIT : How to prepare input data for my crystal ?
See, for example, e-mail#1,#2,#3,#4.
Please note also,
- the possibility to enter directly fractions (like 1/3 or 2/3) and square roots (like sqrt(0.75) ) in the input file (from v.4.x.x): please refer to the release_note.

- Tips to use ABINIT : Energy selective charge density
See the original post, and the follow-ups (#1,#2).

- Tips to use ABINIT : Bandstructure: why my output includes fewer k-points than I expected ?
The default value is limited to 50. Set prtvol as 10 (and prteig as 1 for v.4.3.3, v.4.4.x and the newer versions). (e-mail).

- Tips to use ABINIT : Geometry constraints for selected atoms in geometry optimization/Molecular Dynamics
See the e-mails, #1 and #2.

- Tips to use ABINIT : cut3d: Atomic Sphere Analysis of a wavefunction for selected kpt/band
See the e-mails, #1 and #2.

- Tips to use ABINIT : Piezoelectric calculation
See the e-mails, #1 and #2.

- Tips to use ABINIT : Geometry optimization Under Pressure
Use "strtarget": more specifically, see the e-mail #1.
((other tips, to be added))

- Trouble shooting: Reading old WF/DEN/POT files with v3.4(and later)
See this announce message.

- Trouble shooting: Error in reading my input file
Please note that one-line should be not more than 99 characters. See this e-mail.

- Trouble shooting: Fermi energy is not printed out ?
Read e-mail#1 and #2.

- Trouble shooting: Negative value of DOS ?
See, for example, this.

- Trouble shooting: Tetrahedron method
See, for example, e-mail#1,#2,#3, ...

- Trouble shooting: PAW method
See, for example, e-mail#1,#2,

- Trouble shooting: unit of oscillator strengths?
See, for example, this. Please be careful in old ABINIT versions: Corrected in v4.0.3, v3.4.4
and v3.3.6 (and later).

- Trouble shooting: latest definition of Bohr in Angstrome
(from P.Thibaudeau's mail, also from D.C.Allan's mail on 'developer' ML)
The value of the Bohr radius given from ABINIT 3.3 was updated from the well known article of K.Hagiwara et al. Physical Review D 66 010001 (2002) page 77.
The recommended value of the Bohr radius in 2002 edition was 0.5291772083(19)
In 1998, the Bohr radius value was 0.5291772083(24) from C.Caso et al. The European Physical Journal C3 (1998) 1.
The first updated value of 0.5291772083(19) was in 1999 edition.

- Trouble shooting: What is IFC ?
Read this.

- Trouble shooting: I cannot download a file "foo" from "ftp.abinit.org/pub/incoming/". Why ?
This is because security reason. Read this to download.

- Trouble shooting: Why are different symmetries assigned by different versions of ABINIT ?
You might use the obsolete version of ABINIT ? Please use the latest versions.
(See, for example, e-mail#1,#2 )

- Trouble shooting: Why do ABINIT and other calculation methods produce different results ?
See, for example, e-mail#1(reply to this e-mail), #2.
(To be added... Any suggestions ?)

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