Re: [QE-users] Is pw2wannier90.f90 not up-to-date with the one in wannier90 source code?

2020-06-25 Thread Giovanni Pizzi 
Dear Hongyi,

If you use the ‘develop’ branch of QE, the version you find in the git of QE is 
the most recent.

Here is the history:
https://gitlab.com/QEF/q-e/-/commits/develop/PP/src/pw2wannier90.f90
The new diff is in these two commits:
https://gitlab.com/QEF/q-e/-/commit/6147076521a62437068100e6fa5a36898061a482
https://gitlab.com/QEF/q-e/-/commit/ca5334bdb05e4fe85ec1eac182f352cddd365cd8

If you use the released version 6.5, you might want to use the one from 
Wannier90 instead.

In the Wannier90 repo we just keep patch versions to be applied to already 
released versions of QE, to ‘backport’ new functionality.
The code in the develop branch of QE should be at the most recent version in 
general (so it’s included in future releases).

Best,
Giovanni



--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 23 Jun 2020, at 06:55, Hongyi Zhao 
mailto:hongyi.z...@gmail.com>> wrote:

Hi,

I noticed that the pw2wannier90.f90 in q-e is different from the one
shipped with wannier90 source code:

werner@X10DAi-01:~/Public/hpc/tools/wannier90.git/pwscf/v6.5$ diff
pw2wannier90.f90 ../../../../q-e/q-e.git/PP/src/pw2wannier90.f90 | wc
   4221759   14680

Should I replace it with the one in wannier90 while compiling q-e? Any
hints for this problem?
--
Hongyi Zhao mailto:hongyi.z...@gmail.com>>
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Re: [QE-users] k-points and path for Band structure calculation

2020-06-03 Thread Giovanni Pizzi 
Dear Chaman,

1. Yes. Actually, the band paths are just conventions, and try to pass through 
all points and lines that have some symmetry.
So, the “suggested” band paths depend a lot on the lattice (and actually also, 
in some cases, on the space group, if you want to cover all inequivalent lines, 
as we discuss in [1]).

The band structure is not affected by the path you choose (but of course, by 
choosing a different path, you’ll see different bands).

2. It’s up to you. The ones of wikipedia cover a more complete path, but in 
many cases the relevant features (e.g. lowest conduction band, highest valence 
band, …) might only appear for a given material along a subset of the lines, so 
you can decide show show less paths if you know the material and what you are 
doing.
If you are unsure, I suggest to use our seekpath tool at 
https://www.materialscloud.org/work/tools/seekpath - this will also standardise 
the cell and check the spacegroup symmetry, and e.g. distinguish between hP1 
and hP2 (the path that you/wikipedia report is for what we call hP2; hP1 needs 
an additional segment K-H_2 that is for some space groups is not equivalent to 
K-H; our paper [1] explains more about this).

3. I don’t know. In general they use a shorter path and this is OK. The only 
thing that I’m not sure about is what is the U point for them, as this is not a 
standard point for a hexagonal cell. I didn’t have the time to check the paper 
to see if they say what U is. However, note that at U most bands do not have 
extrema (only one band has a minimum).

So my guess, now that I look better at it, they might be just refolding the 
band structure and using the names of the letters from the cubic FCC lattice, 
refolded on the hexagonal lattice, and this might explain the U point (that 
exists in cF lattices).

However, to confirm this, you will need to check the refolding and try to 
reproduce the band structure, to know if this is the correct interpretation (or 
check if they explain more in the paper).

Hope this helps,
Giovanni Pizzi


[1] Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram 
paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017). DOI: 
10.1016/j.commatsci.2016.10.015<http://doi.org/10.1016/j.commatsci.2016.10.015>


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http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 26 May 2020, at 17:15, Chaman Gupta mailto:cha...@uw.edu>> 
wrote:

Hey everyone,

I am trying to study the effect of pressure on the band structure of 'Si - 
simple hexagonal (Phase V)', which is stable between 17 to 30 GPa (approx.)

Here is a paper published in Nature 
(https://www.nature.com/articles/s41586-020-2150-y), which has a figure with 
the band structure of Hex-Si (image is attached). The image has the following 
path  " A - Gamma - M - U - L ".

IMAGE 1 IS 
HERE<https://drive.google.com/file/d/1zaJSjv3RX3gy87NTuBV5AjkJysW7pdOZ/view?usp=sharing>

When I looked for BZ1 and the path to take for a simple hexagonal structure, I 
came across this link ( https://en.wikipedia.org/wiki/Brillouin_zone). It 
mentions the path to be "Gamma - M - K - Gamma - A - L - H - A|L - M|K - H"

My questions:

1. From what I understand, the path and symmetry points are dependent on the 
type of lattice, and highly affect the band structure. Is this statement right 
or wrong?

2. Which k-points/ High symmetry points/ BZ1/ path should I use for my band 
structure calculation?

3. Is it possible, by any chance the author of this Nature paper, might have 
used the wrong k-points? Or should I use what they have used?

Thanks for the help.


Regards,

Chaman Gupta
Graduate Research Student, Novosselov Research 
Group<http://depts.washington.edu/nrglab/>, UW
Graduate Research Student, Pauzauskie Research 
Group<https://depts.washington.edu/pzlab/wordpress/>, UW
University of Washington Seattle, M.S. in Mechanical Engineering
IIT Kharagpur, B.Tech in Metallurgical and Materials Engineering
Linked In<https://www.linkedin.com/in/professorchamangupta> | 
Email<mailto:cha...@uw.edu> | P: +1 (206) 383-3514
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[QE-users] Newly-engineered Materials Cloud Archive unveiled

2020-05-27 Thread Giovanni Pizzi 
Dear Quantum ESPRESSO users,
we would like to announce the launch of a newly engineered Materials Cloud 
Archive<https://archive.materialscloud.org/>, now powered by the same Invenio 
framework as the massive Zenodo<https://zenodo.org/> repository at CERN.

The Materials Cloud Archive<https://archive.materialscloud.org/>, active since 
March 2017, is a public, free, open-access repository for research data and 
tools in computational materials science and in related experimental efforts, 
inspired by the archive initiatives for preprints. It provides the capability 
to upload and persist arbitrary data records from anyone in the community with 
a minimum guaranteed 10-year retention time per record. Currently, 0.5 
petabytes are already allocated; the  limits for standard submissions are of 5 
GB for data sets in any format, and of 50 GB for AiiDA databases; moderators 
can approve larger data sets upon request. Each entry is assigned a globally 
unique and persistent digital object identifier (DOI) and harvestable metadata. 
The new Invenio platform makes it easier for authors to submit and later update 
data records, provides full-text searches, and powers streamlined workflows for 
content moderation.

The Archive is an integral part of the Materials 
Cloud<https://www.materialscloud.org/> FAIR data infrastructure, in partnership 
with several European and national centres - these include the 
MaX<http://www.max-centre.eu/> Centre of Excellence, the  
MARVEL<https://nccr-marvel.ch/> NCCR, the H2020 
MarketPlace<https://www.the-marketplace-project.eu/>, 
NFFA<http://www.nffa.eu/>, and Intersect<http://intersect-project.eu/> 
projects, EMMC<https://emmc.info/>, 
swissuniversities<https://www.materialscloud.org/swissuniversities>, 
PASC<https://www.pasc-ch.org/>, and OSSCAR<https://www.osscar.org/>. It is a 
recommended repository for Nature’s Scientific 
Data<https://www.nature.com/sdata/policies/repositories#materials>, it is 
indexed by FAIRsharing<https://fairsharing.org/biodbcore-001089/>, Google 
Dataset 
Search<https://datasetsearch.research.google.com/search?query=Materials%20Cloud>
 and EOSC-hub<https://www.eosc-hub.eu/>/EUDAT<https://www.eudat.eu/>’s service 
B2FIND<http://b2find.eudat.eu/group/materialscloud>, and it is registered on 
re3data<https://www.re3data.org/repository/r3d100012611>. Finally, it is an 
official implementation 
network<https://www.go-fair.org/implementation-networks/overview/materials-cloud/>
 of the GO FAIR initiative<https://www.go-fair.org/>.

More information on the Materials Cloud integration of data, workflows and 
codes can be found in L. Talirz et al., Materials Cloud, a platform for open 
computational science, arXiv:2003.12510 
(2020)<https://arxiv.org/abs/2003.12510> and in S. Huber et al., AiiDA 1.0, a 
scalable computational infrastructure for automated reproducible workflows and 
data provenance, arXiv:2003.12476 (2020)<https://arxiv.org/abs/2003.12476>.

The new Materials Cloud Archive infrastructure has been unveiled today 
(Wednesday 27th May 2020), during the MaX 
webinar<http://www.max-centre.eu/webinar/managing-simplifying-and-disseminating-high-throughput-computational-materials-science-aiida>
 (part of the ongoing MaX webinar series<http://www.max-centre.eu/webinar> on 
advances toward exascale computing) that focused on FAIR and reproducible 
high-throughput computational science as enabled by AiiDA and AiiDA lab, 
Quantum ESPRESSO and SIRIUS, and the Materials Cloud Archive. Videos of the 
presentations will be available online from tomorrow (28th May) on the webpage 
of the 
event<http://www.max-centre.eu/webinar/managing-simplifying-and-disseminating-high-throughput-computational-materials-science-aiida>.

With warmest regards,

Giovanni Pizzi, Nicola Marzari, and the Materials Cloud team

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Re: [QE-users] POSCAR to QE input

2020-05-06 Thread Giovanni Pizzi 
Hi,
If you don’t want to run from the command line, or don’t want to install code, 
you can also use directly the web tool "Quantum ESPRESSO input generator" that 
we have published on the Materials Cloud:
https://www.materialscloud.org/work/tools/qeinputgenerator

We have already interfaced it with the ASE parser to read VASP POSCAR files.

In addition to providing you the QE input, the input generator will also 
suggest you good initial parameters and pseudos for your simulation - we have 
tested them, but please provide feedback as indicated on the page if you feel 
the suggested values for pseudos and cutoffs (from the 
SSSP<https://www.materialscloud.org/discover/sssp/>), k-points, smearing, 
starting magnetisation … are not optimal.

Best,
Giovanni

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi



On 6 May 2020, at 11:29, Hongyi Zhao 
mailto:hongyi.z...@gmail.com>> wrote:



Offermans Willem mailto:willem.offerm...@vito.be>> 
于2020年5月6日周三 下午3:44写道：
Hi Poonam Sharma and QE friends,

You might consider using ASE (https://wiki.fysik.dtu.dk/ase/) for this.

From the top of my head:

ase convert -i vasp -o espresso POSCAR system.pwi

It's used as follows, say for printing on stdout:

$ ase convert -i vasp -o espresso-in FeS.POSCAR -

Regards

or something similar.

Try at least the following commands for information:

ase convert --help

ase info --formats



Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

willem.offerm...@vito.be<mailto:willem.offerm...@vito.be>



On 6 May 2020, at 07:13, Poonam Kaushik 
mailto:poonamkaushi...@gmail.com>> wrote:

Dear all,
I want to convert a POSCAR file into the QE input file. I would be very 
grateful if somebody helps or give suggestions.
Fe1 S1
   1.
 5.9487492159093023   -0.   -0.
-2.97437460795465115.15176794171171260.
-0.0.   11.7211034581915818
   Fe   S
1212
Direct
  0.3954866316692124  0.0721204949184797  0.1217724210678790
  0.9278795160815250  0.3233661487507409  0.1217724210678790
  0.6766338512492591  0.6045133683307876  0.1217724210678790
  0.3954866316692124  0.0721204949184797  0.3782275859321179
  0.9278795160815250  0.3233661487507409  0.3782275859321179
  0.6766338512492591  0.6045133683307876  0.3782275859321179
  0.0721204949184797  0.3954866316692124  0.8782275859321180
  0.3233661487507409  0.9278795160815250  0.8782275859321180
  0.6045133683307876  0.6766338512492591  0.8782275859321180
  0.0721204949184797  0.3954866316692124  0.6217724140678820
  0.3233661487507409  0.9278795160815250  0.6217724140678820
  0.6045133683307876  0.6766338512492591  0.6217724140678820
 -0. -0.  0.
 -0. -0.  0.5000
  0.33342996  0.66687029  0.0251416953082458
  0.33342996  0.66687029  0.4748582936917498
  0.66687029  0.33342996  0.9748582936917498
  0.66687029  0.33342996  0.5251417063082502
  0.6643064194527374  0.477489745914  0.2500
  0.522750254107  0.6643586704781460  0.2500
  0.3356412995218515  0.3356935805472627  0.2500
  0.477489745914  0.6643064194527374  0.7500
  0.6643586704781460  0.522750254107  0.7500
  0.3356935805472627  0.3356412995218515  0.7500
Thanks,
Poonam S



-
Poonam Sharma
Research Scholar
Department of Physics
Indian Institute of Technology Bombay
Mumbai - 400076
India.

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[QE-users] Videos of the "Virtual Edition" Wannier90 School online on Materials Cloud Learn

2020-04-01 Thread Giovanni Pizzi 
Dear all,

We are glad to inform you that the video recordings of the first "Virtual 
Edition” of the Wannier90 School [1] are now all available in the Learn section 
of Materials Cloud, at this link:

https://www.materialscloud.org/learn/sections/C8ad91/wannier90-v3-0-school-virtual-edition-2020

Beside the videos, the Learn section also includes:
- the slides of the presentations;
- the list of all questions asked during the presentations, with detailed 
replies by the speakers;
- all tutorial hands-on materials.

In particular, the tutorial was run on the "Quantum Mobile" Virtual 
Machine<https://www.materialscloud.org/work/quantum-mobile> that made it very 
easy for all 30+ participants to quickly get started with the various codes 
presented (Quantum ESPRESSO, Wannier90, WannierTools, AiiDA, EPW, ...) with 
almost zero setup time.

As an additional benefit, anybody can download again the Quantum Mobile [2] and 
run the same tutorials, even if they could not attend the event.

We believe that these virtual events can be very effective and can become a 
model for the future, even when travel restrictions will be lifted, with the 
additional advantages of allowing a broader and more diverse audience, and of 
reducing our carbon footprint, under the slogan "less carbon, more silicon"!

Best regards,
Giovanni Pizzi, on behalf of all event organisers

[1] http://www.wannier.org/events/school-2020-virtual-edition/
[2] The tutorial was run using version 20.03.1: 
https://github.com/marvel-nccr/quantum-mobile/releases/tag/20.03.1

PS: sorry if you received this message multiple times, but we felt this could 
be relevant also to the Quantum ESPRESSO community

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Re: [QE-users] Band structure with hybrid functionals

2019-10-27 Thread Giovanni Pizzi 
Hi Dominik,
Did you try to check if you could use Wannier90 to get an interpolated band 
structure? You might also look into our recent preprint where we discuss an 
algorithm to compute the Wannier functions automatically, based on the SCDM 
method: https://arxiv.org/abs/1909.00433 so you don’t even need to find the 
correct initial projections.

I would be interested to know if this approach works for you.

Best,
Giovanni

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 26 Oct 2019, at 23:21, Dominik Gresch 
mailto:gres...@gmx.ch>> wrote:

Dear QE users,

I am trying to calculate the band structure of a material with hybrid 
functionals. Since it is not possible to perform an NSCF run in that case, the 
desired k-points should be included in the SCF calculation. Since increasing 
the k-point mesh as a whole is rather expensive, I tried explicitly setting the 
list of k-points (in "crystal" mode), and then appending the desired k-points 
for the band structure as points with zero weight [0].

However, when trying this trick, I am faced with the following error:
%%
Error in routine exx_grid_init (117994):
k + q is not an S*k
%%

My questions are as follows:
- does anyone have experience in computing the band structure with hybrids, and 
if so, is this the right approach?
- what is the nature of this error, and is there some work-around?

Thank you and best regards,
Dominik Gresch
--
Microsoft Research

[0] I am familiar with using this technique from experience using VASP 
(described here: https://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure)
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Re: [QE-users] Compilation on a server ends with error 1

2019-04-09 Thread Giovanni Pizzi 
Dear Fabio,
Quantum ESPRESSO automatically downloads Wannier90 and prepares a make.inc file 
inside the folder it creates.
In there, you can change the variables defining the compilers to use.
Before recompiling, I suggest to do a ‘make clean’ inside the Wannier90 folder 
to remove old compiled objects, if any.

Best,
Giovanni

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Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi



On 9 Apr 2019, at 18:39, Paolo Giannozzi 
mailto:p.gianno...@gmail.com>> wrote:

Wannier90 uses its own build system, so you will have to figure out what has to 
be changed there

Paoo

On Tue, Apr 9, 2019 at 5:59 PM Fabio Costa 
mailto:fabiocos...@hotmail.com>> wrote:
Dear Pietro

Thank you very much for your help so far, things are starting to work out. Your 
guess was actually right, and the mpif90 was using the old version. After a few 
attempts, The installation was successful, and now I have both mpif90 and 
gfortran v-5.4 .

I still need to indicate the path of these updated executables when compiling 
QE, so Im starting with the command "./configure 
MPIF90=/home/fabio/local/bin/mpif90 F90=/home/fabio/local/bin/gfortran ". This 
step runs successfully, but when making pw, but eventually it stops with a 
fatal error warning, about some fox module that could not be opened because it 
was created with a different GNU fortran version. At this point I found out 
that inside make.inc, the path I provided to mpif90 was accurate, but F90 
contained only gfortran, which I think would link to the native (not-updated) 
executable. To correct this, I added to F90 the path to the updated executable. 
After this change, the make pw, ph and w90 finish successfully, and after some 
quick tests, it seems that the executables are running as expected (no more 
segmentation faults).

Unfortunately, when I try to make epw, the fatal error happens again 
(https://imgur.com/ukHDZYc). This should be happening because something was 
compiled with the old gfortran, even when I manually changed the MPIF90 and F90 
to link to the updated versions. Do you have any insights on what could have 
went wrong?

Thanks for the assistance

Fábio Costa
 MSc student in physics
 Federal University of Bahia, Brazil


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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

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[QE-users] Wannier90 v3.0.0 new major release

2019-02-27 Thread Giovanni Pizzi 
Dear all,

After two years in the making, we are very proud to announce a new major 
release of Wannier90, v3.0.0. This can be downloaded from 
http://www.wannier.org/download/

Moreover, this new release will be fully integrated with the upcoming release 
of Quantum ESPRESSO (by just running ‘make w90’).

This work has been possible also thanks to the many contributions of various 
researchers, who are listed on the GitHub home 
page<https://github.com/wannier-developers/wannier90> of the project.

The list of all changes can be found on the 
CHANGELOG<https://github.com/wannier-developers/wannier90/blob/v3.0.0/CHANGELOG.md>
 and the list of all features of the code can be found on the Features 
page<http://www.wannier.org/features/> of the website.

Together with this new version, we also redesigned the Wannier website. You can 
find the new version at the usual address: 
http://www.wannier.org<http://www.wannier.org/> (you might need to clear your 
browser cache to see the new website).

Furthermore, a paper describing the new functionality of this new major release 
is in preparation. We will keep you posted as soon as it is published.

Cheers,
The Wannier90 developer group (Giovanni Pizzi, Valerio Vitale, Nicola Marzari, 
David Vanderbilt, Ivo Souza, Arash Mostofi, Jonathan Yates)

P.S.: for the developers of the interfaces to the various codes: we are more 
than happy to be in touch with you to discuss the new interface features and 
how to integrate these in your interface codes. In particular, all the new 
functionality is already integrated in pw2wannier90.x, the interface between 
Quantum ESPRESSO and Wannier90, and will be distributed with the upcoming 
Quantum ESPRESSO release.

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[QE-users] Materials Cloud is now a recommended repository of Nature Research’s Scientific Data

2018-09-06 Thread Giovanni Pizzi 
Dear colleagues,

We are very pleased to announce a collaboration between Materials 
Cloud and the Nature Research data journal 
Scientific Data.

Materials Cloud is an Open Science Platform 
offering educational, research, and archiving tools; simulation software and 
services; and curated and raw data. It is a non-profit service, developed and 
supported by the Swiss NCCR MARVEL, the European H2020 
MaX Centre of Excellence, as well as by a number of 
other partners.

Scientific Data is an open access journal 
focused on a new article type, the ‘Data Descriptor’, which has been 
specifically designed to publish peer-reviewed research data in an accessible 
way, so as to facilitate its interpretation and reuse. Publishing Data 
Descriptors enables data producers and curators to gain appropriate credit for 
their work, whilst also promoting reproducible research.

Today Materials Cloud joins a wide range of data repositories, representing 
research data from across the entire scientific spectrum. Materials Cloud has 
been approved by Scientific Data as providing stable archiving and long-term 
preservation of materials science datasets.

Researchers now have the opportunity to deposit materials science data to 
Materials Cloud, whilst submitting a Data Descriptor to Scientific Data. Upon 
publication, Materials Cloud will ensure the data is made freely accessible and 
preserved for the long term benefit of the research community.



We are excited to be contributing, with AiiDA and the 
Materials Cloud, to the open data effort in 
Computational Materials Science.



Best regards,

The Materials Cloud team

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Re: [QE-users] Quantum Espresso on Amazon Web Services

2018-09-06 Thread Giovanni Pizzi 
Hi,
Give a look to this article:
https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/t2-credits-baseline-concepts.html

It’s possible that you have one of these VMs, that on average deliver only a 
low (even only down to 5%) performance than the actual CPU performance (it 
might seem fast at the first run, if you didn’t run anything, but the algorithm 
of CPU credits will make runs be slow, eventually).

Also, crashes might be due to limited RAM.

HTH,

Giovanni

On 5 Sep 2018, at 10:48, Uri Argaman 
mailto:argam...@post.bgu.ac.il>> wrote:

Dear QE users and devalopers
I'm running QE on Amazon Web Services (AWS) and I see that the run times are 
very bad compared to other systems that I use and I also encountered crashes 
which I cannot understand the reason for them. Does anyone work on AWS and know 
something about the performance and special compilation issues?
Thank you
Uri Argaman
Ben-Gurion University
Israel
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[QE-users] Two open positions for computational materials scientists/software scientists on data and services (THEOS, EPFL)

2018-07-03 Thread Giovanni Pizzi 
Dear all,

Two positions for computational materials scientists/software scientists are 
available at the École Polytechnique Fédérale de Lausanne (EPFL, Lausanne, 
Switzerland) in the group of Prof. Nicola Marzari. The positions are funded by 
the new H2020 MarketPlace project (https://www.the-marketplace-project.eu/, 
2018-2022, 9.2 M€) aimed at developing a single entry point for all industrial 
and academic materials modelling activities in Europe. EPFL will lead the work 
package on "Data and Modelling Services".

Outstanding candidates are sought with a background in the physical sciences 
(typically, physics, chemistry, and materials science) alongside with strong 
programming abilities and work ethics.
Natural synergies will be present with the AiiDA (http://aiida.net) and 
Materials Cloud (http://materialscloud.org) teams.

Candidates should be interested in working in a field at the intersection 
between academia and industry, striving to close the gap between the two 
domains, making state-of-the-art academic modelling tools more easily available 
for industry, and promoting the European Open Science Platform. For interested 
applicants, scientific research challenges can also be incorporated where they 
align with the objectives of the MarketPlace project.

For more information on the position, the expected background and requirements, 
and details on how to apply, please refer to the official advertisement: 
http://theossrv1.epfl.ch/uploads/Main/Openings/2018_07_MarketPlace_materials_scientist.pdf

Best,

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

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[QE-users] Tutorial on high-throughput computations using AiIDA: deadline approaching

2018-04-18 Thread Giovanni Pizzi 

Dear all,

we would like to remind you that the deadline of the following AiiDA 
tutorial is approaching (April 30th).
In the tutorial, the AiiDA developers will explain how to use the AiiDA 
code (in combination with a number of quantum codes, including Quantum 
ESPRESSO) to perform high-throughput computations, with particular focus 
also on the new features of the new AiiDA version. The tutorial also 
includes two talks on actual high-throughput research projects using 
AiiDA (see below).


The tutorial is free of charge for the selected participants, and some 
travel grants are also available.


Further information can be found at the tutorial's web-page: 
https://events.prace-ri.eu/event/709/overview


Best regards,
Giovanni Pizzi

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi


-
PRACE-MaX Tutorial on high-throughput computations: general methods and 
applications using AiiDA@Cineca


Description:
AiiDA is a flexible and scalable informatics infrastructure to manage, 
preserve, and disseminate the simulations, data, and workflows of 
modern-day computational science. The PRACE-MaX tutorial is targeted at 
about 40 students, postdocs and researchers interested in applying 
high-throughput computations in their research, and in particular to 
those interested in learning how to use the AiiDA platform.


The tutorial will be held by members of the AiiDA developers team 
(Sebastiaan Huber, Leonid Kahle, Giovanni Pizzi Martin Uhrin and Spyros 
Zoupanos). Moreover, two scientific talks will be given by Giovanni 
Pizzi (Discovering two-dimensional materials from high-throughput 
computational exfoliation of experimentally known compounds) and Leonid 
Kahle (Fast screening of solid-state lithium-ion conductors) on their 
research using AiiDA and high-throughput.


Skills:
By the end of the tutorial the students should:
• have an in depth understanding of AiiDA and how it can be used to 
facilitate and automatise their research

• know how to setup and manage AiiDA
• know how to submit calculations, write and submit workflows
• know how to query their results and manage their high-throughput research

Target Audience:
Researchers in materials science, chemistry and related fields 
interested in applying high-throughput computations in their research, 
and in particular to those interested in learning how to use the AiiDA 
platform.


Poster session:
Participants are typically expected to bring a poster. Please send an 
email to corsi@cineca.it <mailto:corsi@cineca.it> with subject 
"PATC - AiiDA tutorial - Poster session" indicating the title and a 
brief abstract (max 1500 characters).


Pre-requisites:
• knowledge of Linux;
• familiarity with the use of a job scheduler (slurm, torque, pbspro, 
sge, ...);
• knowledge of Python will be valuable (please indicate your level in 
the registration form);

• knowledge of Quantum ESPRESSO will be valuable.

Grant:
Registration and attendance are free of charge for the selected 
applicants. The lunch for the three days will be offered to all the 
participants and some grants are available. In order to be eligible for 
a grant, you should not be funded by your institution and you should 
also work & live outside the Bologna area. The grant will be 300 euros 
for students working and living outside Italy and 150 euros for students 
working and living in Italy (outside Bologna area). It will be provided 
after the end of the tutorial, after a certified attendance to the 
lectures (minimum 80%) and some proof regarding the place of work or 
residence.


Further information about how to request the grant, will be provided at 
the confirmation of the course: about 3 weeks before the starting date.


Venue:
CINECA in Casalecchio di Reno (near Bologna). More information on how to 
reach it can be found at the event page 
https://events.prace-ri.eu/event/709/overview


Selection:
The number of participants is limited to 40 students. Applicants will be 
selected according to their experience qualification and scientific 
interest BASED ON WHAT WRITTEN IN THE "Reason for participation" FIELD 
OF THE REGISTRATION FORM. Please indicate your Python level in the 
registration form and if you would like to attend a preliminary Python 
course the days before the tutorial.


Social dinner:
An evening buffet will be offered by the tutorial sponsors to all 
participants on the second day of the course.


Important dates:
Start of registration: February, 3rd 2018
End of registration: April, 30th 2018
Contact of successful applicants: May, 7th 2018

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[Pw_forum] Quantum Mobile virtual machine and AiiDA 0.10.0

2017-11-21 Thread Giovanni Pizzi 
Dear all,

Yesterday we have released:

  *   the first version of the Quantum Mobile Virtual Machine (v. 17.11.0), 
supported by the MARVEL NCCR (http://marvel-nccr.ch) and the MaX H2020 Centre 
of Excellence (http://max-centre.eu). You can find all instructions to download 
it here: https://github.com/marvel-nccr/quantum-mobile/releases/tag/17.11.0

Quantum Mobile is a virtual machine based on Ubuntu Linux that comes with a 
collection of quantum simulation codes including Quantum ESPRESSO, Yambo, 
Fleur, Siesta, cp2k. All codes are set up and ready to be used through AiiDA.

Quantum Mobile may be useful for exercises in physics, chemistry and materials 
science courses, for running quantum simulations without any setup, for 
experimenting with new codes, but also for managing production simulations on 
external supercomputers through AiiDA.
  *   AiiDA v0.10.0: You can find more information at our 
download<http://www.aiida.net/download/> page. A detailed overview of a all the 
changes can be found in the change log on 
GitHub<https://github.com/aiidateam/aiida_core/blob/v0.10.0/CHANGELOG.md>.


Feel free to download and share!
All the best,

Giovanni Pizzi, on behalf of the whole AiiDA Team


--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

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[Pw_forum] Open position for a software engineer/web developer - MARVEL, EPFL, Switzerland

2017-04-28 Thread Giovanni Pizzi 
Dear all,

an open position for a software engineer/web developer is available at EPFL 
(Lausanne, Switzerland) in the MARVEL NCCR (http://marvel-nccr.ch).

For interested applicants scientific research challenges can also be 
incorporated in the effort, but this is not a requirement.

Excellent candidates are sought with experience in the development of complex 
web architectures powered by cloud technologies, to support the development and 
deployment of the Materials Cloud 
(www.materialscloud.org<http://www.materialscloud.org>), a web portal for 
computational materials science powered by AiiDA 
(www.aiida.net<http://www.aiida.net>).

AiiDA is a materials’ informatics framework that acts as a flexible and 
scalable infrastructure to manage high-throughput computations; Materials Cloud 
is a portal for computational materials science and an online cloud platform. 
Such infrastructure underpins the efforts of the MARVEL NCCR; close 
collaboration takes also place with the H2020 Centre of Excellence MaX for 
"Materials Design at the Exascale" (http://www.max-centre.eu/).

The project will focus on research case studies for the existing Materials 
Cloud platform, with primary focus on the portal frontend (in AngularJS) and 
optimization of its user interface and its ergonomic design, as well as support 
for the backend development (Python+Flask).

The software engineer would work with a team of 10+ PhD students, postdocs, and 
software specialists with diverse backgrounds (physicists, chemists, materials 
scientists and computer scientists) contributing both to AiiDA and the 
Materials Cloud.

Candidates should submit 1) a full CV, including contacts for at least two 
references, and 2) a cover letter of intent. These documents (PDF only) should 
be emailed to both giovanni.pi...@epfl.ch<mailto:giovanni.pi...@epfl.ch> and 
berend.s...@epfl.ch<mailto:berend.s...@epfl.ch>, with the exact text "MARVEL 
Web Engineer" in the subject line.
For best consideration, applications should be submitted by May 31st; the 
position will remain open until filled.

Duration of the contract: 1-year, renewable.

For additional details on this opening, see 
http://theossrv1.epfl.ch/uploads/Main/Openings/2017_04_MARVEL_MaterialsCloud_Web_Engineer.pdf


Best,
Giovanni Pizzi

--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

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Re: [Pw_forum] high-symmetry point is wrong in the output of bands.x

2017-04-13 Thread Giovanni Pizzi 
Hi,
I think both values are correct, depending on which units one is referring to.

X is (1/2,/1/2,0) (and equivalent) in *scaled* coordinates in the *primitive* 
cell,
But is along {1,0,0} when expressed in cartesian coordinates, or w.r.t. the 
*conventional* cell.

The value printed by bands.x is consistent with the units/choices of the code.

Best,

Giovanni

P.S.: You can see an interactive 3D visualisation of the BZ at 
http://materialscloud.org/tools/seekpath
(Choose the example "cF2 [with inversion]” for this specific case).



--
Giovanni Pizzi
Theory and Simulation of Materials and MARVEL, EPFL
http://people.epfl.ch/giovanni.pizzi
http://nccr-marvel.ch/en/people/profile/giovanni-pizzi

On 13 Apr 2017, at 10:41, Paolo Giannozzi 
<p.gianno...@gmail.com<mailto:p.gianno...@gmail.com>> wrote:

On Thu, Apr 13, 2017 at 3:11 AM, balabi <bal...@qq.com<mailto:bal...@qq.com>> 
wrote:

I am using QE6.1. I found the high symmetry point in the output of bands.x
is not right.

sure? your system has a FCC lattice (ibrav=2). Find a picture of the
Brillouin Zone and of high-symmetry points, for instance this one:
http://www.iue.tuwien.ac.at/phd/dhar/node18.html
Where do you see that X is (1/2, 1/2, 0) ?

Paolo

Take copper as an example, set k path as below in bands calcuation

K_POINTS tpiba_b
2
gG 20
X 1

a possible X coordinate should be "0.5 0.5 0". However, the output of
bands.x is

high-symmetry point:  0. 0. 0.   x coordinate   0.
high-symmetry point:  0. 1. 0.   x coordinate   1.

"0 1 0" is definitely not right for X point.

The reason I want to use high symmetry point information is that I want to
write an automatic k path transformation tool from PW to wannier90 input win
file.

below are input files for test
---
copper.scf.in
--

   calculation='scf'
   restart_mode='from_scratch',
pseudo_dir = '/mnt/e/DFT_code/QE/pseudo',
   outdir='./'
   prefix='cu'
/

   ibrav = 2, celldm(1) =6.822, nat= 1, ntyp= 1,
   ecutwfc = 30.0
   occupations='smearing', smearing='cold', degauss=0.02
/

/
ATOMIC_SPECIES
Cu 63.546 Cu.pz-n-van_ak.UPF
ATOMIC_POSITIONS
Cu 0.0 0.0 0.0
K_POINTS (automatic)
8 8 8 0 0 0
--
copper.bands.in
---

   calculation='bands'
   restart_mode='from_scratch',
pseudo_dir = '/mnt/e/DFT_code/QE/pseudo',
   outdir='./'
   prefix='cu'
/

   ibrav = 2, celldm(1) =6.822, nat= 1, ntyp= 1,
   ecutwfc = 30.0
   occupations='smearing', smearing='cold', degauss=0.02
   nbnd=12
/

/
ATOMIC_SPECIES
Cu 55.85 Cu.pz-n-van_ak.UPF
ATOMIC_POSITIONS
Cu 0.0 0.0 0.0
K_POINTS tpiba_b
2
gG 20
X 1
--
bands.x.in


outdir='./',
prefix='cu',
filband='bands.dat',
/

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[Pw_forum] AiiDA tutorial - Lausanne, May 2017

2017-01-09 Thread Giovanni Pizzi 

Dear all,

The second edition of the MARVEL/Psi-k/MaX "Tutorial on high-throughput 
computations: general methods and applications using AiiDA" will take 
place on May 29-31, 2017 at EPFL (Lausanne, Switzerland), targeted at 
students, postdocs and researchers interested in applying 
high-throughput computations in their research and interested in 
learning how to use the AiiDA platform.


The program includes a tutorial on the AiiDA code, and invited highlight 
talks from experts in the field of high-throughput computations (Prof. 
T. Bligaard, Stanford University; Prof. M. Fornari, Central Michigan 
University; Prof. C. Pickard, University of Cambridge; Prof. S. Sanvito, 
Trinity College Dublin).


Registration is open *until Feb 26, 2017*. The registration link, 
requirements that must be met by the applicants, and additional 
information can be found here: 
http://nccr-marvel.ch/en/events/aiida-tutorial-may-2017


Thanks to sponsorship from MARVEL/Psi-k/MaX, we can provide financial 
support for the lodging expenses of a limited number of accepted 
participants. All other expenses (travel, food, ...) must be covered by 
the participants themselves. Additional participants can be accepted up 
to the room capacity, but their expenses will not be covered.


Best regards,

The tutorial organizers (Giovanni Pizzi, Fernando Gargiulo, Andrea 
Ferretti, Jens Broeder)



--
Giovanni Pizzi
EPFL STI IMX THEOS
MED2 1326
Station 9
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] MARVEL postdoc in science or engineering: Integration of the nanoporous genome with AiiDA and the Materials Cloud

2016-12-10 Thread Giovanni Pizzi 
Dear all,

An open postdoc position is available at EPFL (Sion and Lausanne, Switzerland) 
in the MARVEL NCCR (http://marvel-nccr.ch).

Excellent candidates are sought with strong experience in the development of 
software and an affinity for big-data approaches.

The candidate will work together with a team of physicists, chemical engineers, 
material scientists and software engineers working on simulations and 
applications of nanoporous materials, or developing/contributing to the AiiDA 
infrastructure (www.aiida.net<http://www.aiida.net>) and the Materials Cloud 
portal.
In particular, the project will focus on extending the AiiDA platform to 
integrate the nanoporous materials genome library as developed in the LSMO 
laboratory, and develop data analysis tools like e.g. similarity matching of 
pore structures.
Besides the integration, the candidate is expected to develop his own research 
program at the interface of the THEOS and LMSO groups.

The position will be co-hosted in the Laboratory for Molecular Simulations 
(LSMO), led by Prof Berend Smit (http://lsmo.epfl.ch/) and the Laboratory for 
Theory and Simulation of Materials, led by Prof Nicola Marzari 
(http://theossrv1.epfl.ch).
The candidate is expected to split his/her time between the two groups (located 
in Sion and Lausanne, respectively).

Candidates should submit a full CV, including contacts for at least two 
references, and a cover letter of intent to 
giovanni.pi...@epfl.ch<mailto:giovanni.pi...@epfl.ch> and 
berend.s...@epfl.ch<mailto:berend.s...@epfl.ch>, with “MARVEL Postdoc position 
– nanoporous genome” in the subject line (PDF attachments only). For best 
consideration applications should be submitted by January 20th 2017, but the 
position will remain open until filled.

Duration of the contract: 1-year, renewable.

For additional details on this opening, see 
http://theossrv1.epfl.ch/uploads/Main/Openings/2016_12_MARVEL_nanoporous.pdf

Best regards,
Giovanni Pizzi

--
Giovanni Pizzi - Research Scientist - THEOS and MARVEL, EPFL
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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Re: [Pw_forum] method to create high-symmetry k-paths?

2016-11-04 Thread Giovanni Pizzi 
Hi,
thanks for your message.

I’d like to add a more detailed explanation for those who are interested in the 
details.
Indeed, our work https://arxiv.org/abs/1602.06402 cites and takes inspiration 
on the paper you mention by Setyawan and Curtarolo (SC). The SC paper was the 
first to introduce the concept of standardisation of crystal structures and 
band paths for high-throughput, and to derive explicitly the coordinates of 
irrational k-points and BZ edges.

Our work was meant to improve some issues of that paper.
A detailed discussion on the improvements can be found in our paper, but the 
most important points are, in my view:

- for some space groups, it is not sufficient to just inspect the Bravais 
lattice. Instead, the path must depend on the spacegroup. The simplest case is 
the simple cubic lattice: if the corresponding symmorphic group does not have 
90degree rotation symmetries (or equivalently mirror symmetries w.r.t. the 
{110} planes), additional lines must be considered, along which the bands will 
differ from the existing paths.
See for example the cP1 example on the SeeK-path website (for spacegroup Pm3), 
or the band plots at the end of our paper.

-  We always use standard k-point letters as defined in the International 
Tables and in the Bilbao Crystallographic Server. Moreover, when new letters 
have to be introduced, then never collide with existing letters from these two 
standard sources.

- We use standard choices and settings for standardization of the crystal cell, 
that are based on standard crystallographic conventions (IT tables, and Parthé 
and Gelato paper [1]). As an an example, in the SC paper, monoclinic lattices 
are chosen to be unique-axis a, while the standard choice is unique-axis b. Or: 
for orthorhombic lattices, SC always choose a> wrote:

Hi,

This research paper might also help, It contains high symettry path for all 
systems.

 link: https://arxiv.org/abs/1004.2974

Regards,
Ghdaiyali Mohammed Kader.
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Re: [Pw_forum] method to create high-symmetry k-paths?

2016-11-03 Thread Giovanni Pizzi 
Dear all,

I would like to mention that I recently released a python tool (called 
SeeK-path) that allows you to get the list of k-points for any 
spacegroup, together with the suggested band path.
You can find the code here: https://github.com/giovannipizzi/seekpath 
and there is also an online tool on the materials cloud website: 
http://materialscloud.org/tools/seekpath

The website is useful for playing with it, but if you want to script it, 
you just need to install the python tool (pip install seekpath), pass 
the structure as input to the seekpath.get_path() function [you can 
parse the Quantum ESPRESSO input structure e.g. with ASE, or with the 
tools in AiiDA] and then write back the results in a file in the format 
you need.

This should be straightforward to code, and in the future I might add 
routines to do this automatically for the most common file formats like 
matdyn (or feel free to fork the code and add the functionality, if you 
want!).

Best,
Giovanni


On 11/03/2016 12:11 PM, Christoph Wolf wrote:
> Dear Lorenzo!
>
> Thank you for your reply! Your work-flow is exactly like mine. I know this
> works quite well but I find the copy-pasting-editing from the bands output a
> bit tedious (yet I am too lazy to make a script...).
>
> Today I found however that the package "PlotPhon" contains a neat script
> written by E.I. Isaev of Linkoping University, Sweden with a quite nice
> generator for k-point paths for a few bravais lattices! It produces a file
> ph.grid that contains exactly what I want.
>
> I will try and see how far it gets me!
>
> Best,
> Chris
>
> Message: 6
> Date: Thu, 03 Nov 2016 09:19:15 +0100
> From: Lorenzo Paulatto <lorenzo.paula...@impmc.upmc.fr>
> Subject: Re: [Pw_forum] method to create high-symmetry k-paths?
> To: PWSCF Forum <pw_forum@pwscf.org>
> Message-ID: <1726820.3nKUJ2z1xf@naquite>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello Christoph,
> what I usually do is I pick the high symmetry points from a paper, or the
> Bilbao crystallographic server, or xcrysden and then I use the method
> "tpiba_b" or "crystal_b" to generate the paths (or q_in_band_form=.true. in
> matdyn.x, when doing phonons). See the K_POINTS section of INPUT_PW.html for
> more details on the syntax, it is quite easy.
>
> hth
>
> On Thursday, November 3, 2016 1:01:05 AM CET Christoph Wolf(??) wrote:
>> Dear all!
>>
>> Sometimes I have to plot the phonon dispersion along a certain k-path
>> (G->X->R?).
>   
>> Usually I pick the k-path in xcrysden, then run a band structure
> calculation
>> with crystal_b, pick the k-path from the out-file and insert it into my
>> matdyn in file. But that procedure, despite working well, is just
>> cumbersome and I was wondering if there is a more direct way to generate
>> the k-path (without coding my own, which I did for cubic but I am worried
>> about other symmetries, weights, ?).
>   
>> Obviously the routine is embedded in QE because it never failed to
> generate
>> a k-path during the band-structure calculation but I was not capable to
>> access it directly!
>   
>> Thank you for your help in advance!
>>
>> Yours,
>> Chris
>>
>> Christoph Wolf
>> Postech University, Pohang, South Korea
>> Dep. Of Materials Science and Engineering
>>
>>
>>
>>
> [http://home.postech.ac.kr/wp-content/themes/postech/images/mail_logo_postec
>> h30.png]
>   30POSTECH
>
>


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EPFL STI IMX THEOS
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Station 9
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] MARVEL/MaX/Psi-k Tutorial on high-throughput computations: general methods and applications using AiiDA

2016-01-12 Thread Giovanni Pizzi 
Dear all,

We are going to hold a MARVEL/MaX/Psi-k "Tutorial on high-throughput 
computations: general methods and applications using AiiDA" on June 22 to 24, 
2016 at EPFL (Lausanne, Switzerland), targeted at students, postdocs and 
researchers interested in applying high-throughput computations in their 
research and interested in learning how to use the AiiDA platform.

The program includes a tutorial on the AiiDA code, and three invited highlight 
talks from experts in the field of high-throughput computations.

Registration is open until Feb 12, 2016. The registration link, requirements 
that must be met by the applicants, and additional information can be found 
here: http://nccr-marvel.ch/en/events/aiida-tutorial-june-2016

Note that lodging expenses of a limited number of accepted participants will be 
covered with a fellowship. All other expenses (travel, food, ...) must be 
covered by the participants themselves. Additional participants can be accepted 
up to the room capacity, but their lodging expenses will not be covered.

Best regards,

The tutorial organisers (Giovanni Pizzi, Andrea Ferretti, Boris Kozinsky)

--
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Room MED2 1326
Station 9
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[Pw_forum] Tutorial on high-throughput computations, and new AiiDA release

2015-12-17 Thread Giovanni Pizzi 

Dear all,

a new version of *AiiDA (v0.5.0) is now available for download*.
You can find more information and download instructions at 
http://www.aiida.net/?page_id=264


Also, we are going to hold a *MARVEL/MaX/Psi-k "Tutorial on 
high-throughput computations: general methods and applications using 
AiiDA"*. The program includes three invited highlight talks from experts 
in the field of high-throughput computations, and a tutorial on the 
AiiDA code.
The tutorial will take place in *Lausanne, Switzerland, from June 22 to 
24, 2016*.
Registration will open in early January; for the time being, if you are 
interested write down the date in you calendar! Lodging expenses of 
accepted participants will also be covered.


Finally, if you are interested in following AiiDA news or in getting 
help with the code, please register to the *AiiDA users' mailing list* 
(very low traffic), following the instructions here: 
http://www.aiida.net/?page_id=356


Best regards,

Giovanni Pizzi on behalf of the whole AiiDA team: 
http://www.aiida.net/?page_id=34




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MED-2.13.26
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[Pw_forum] AiiDA released - a new platform for materials' informatics

2015-06-15 Thread Giovanni Pizzi 
Dear Quantum ESPRESSO users,

we are happy to announce that AiiDA - a materials' informatics Python
platform to manage, store, organize, query and share large amounts of
data, calculations, and workflows - has been recently released and can
be freely downloaded from the website http://www.aiida.net.

A preprint describing AiiDA is available on arXiv at
http://arxiv.org/abs/1504.01163 while extensive code documentation for
users and developers (installation instructions, tutorials, user and
development manuals) is distributed with the code and available
online at

 http://aiida-core.readthedocs.org/en/stable/

The core of the software ("aiida_core") is released under an open-source
MIT license and can be freely downloaded (no registration necessary) from
the AiiDA website or from BitBucket:

 http://www.aiida.net/?page_id=264
 https://bitbucket.org/aiida_team/aiida_core

"aiida_core" is complemented by an extended set of plugins; these are
free and distributed with the code provided you belong to an
academic institution. These plugins provide support for various
simulation packages, including the Quantum ESPRESSO codes pw.x, cp.x,
ph.x, matdyn.x, q2r.x.
This extended version ("aiida_epfl", that includes "aiida_core")
can be obtained from

 http://theossrv1.epfl.ch/aiida_download/

Hoping that you may find AiiDA useful for your research,

Giovanni Pizzi on behalf of the AiiDA team
(http://www.aiida.net/?page_id=34)


-- 
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Post-doctoral Research Scientist
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Station 12
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Phone: +41 21 69 31124

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Re: [Pw_forum] ERROR IN: iotk_scan_tag (iotk_scan.f90:477)

2014-11-21 Thread Giovanni Pizzi 

Dera Vijay Amirthara,
please check this:
http://www.quantum-espresso.org/faq/frequent-errors-during-execution/#5.3

or the results of this:
https://www.google.ch/search?=IOTK+UNRECOVERABLE+site%3Aqe-forge.org=utf-8=utf-8

like
http://qe-forge.org/pipermail/pw_forum/2012-September/099687.html
http://qe-forge.org/pipermail/pw_forum/2012-September/099684.html
http://qe-forge.org/pipermail/pw_forum/2011-February/093813.html
...

(in particular, check if what is written in the first one of these three 
links solves your problem).


Best,
Giovanni

P.S.: please remember to provide also your affiliation when posting on 
this forum.


--
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Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (Bâtiment MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124



On 11/21/2014 11:09 AM, Vijay Amirtharaj A wrote:

Hi,

We are Espresso-5.0.2 and patched with espresso-5.0.2-5.0.3.diff

While running the job, it is running fine. When we are restarting the 
job, below error is coming and i attached make.sys file. Please help 
me to resolve this issue.




# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=2)
# ERROR IN: iotk_scan_tag (iotk_scan.f90:477)
# CVS Revision: 1.23
#
iostat=-1
# ERROR IN: iotk_scan (iotk_scan.f90:821)
# CVS Revision: 1.23
# ERROR IN: iotk_scan_end (iotk_scan.f90:241)
# CVS Revision: 1.23
# foundl

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Regards,

Vijay Amirtharaj A


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Re: [Pw_forum] How can I extract hopping parameters from the output of wannier90

2014-10-12 Thread Giovanni Pizzi 
While the Slater-Koster parameters are real, the Hamiltonian matrix elements 
are complex.
You should study how to build a tight-binding Hamiltonian; one good point to 
start is the original paper by Slater and Koster 
http://journals.aps.org/pr/abstract/10.1103/PhysRev.94.1498
or you can check many solid-state books or any other resource on tight-binding.

Best,
Giovanni

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MXC 340 (Bâtiment MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124





On 11 Oct 2014, at 14:35, Pang Rui wrote:

Dear all
Wannier functions were used in many papers to construct a tight binding
model. The off diaganalization matrix elements were interpreted as the
hopping parameters. However, I found that in most of the times, these
elements were complex numbers. How can I related these complex numbers to
real numbers to parameter a TB model?

Best wishes!
Pang Rui
--
PostDoc
Department of Physics, South University of Science and Technology of China
Shenzhen, Guangdong, PRC, 518500
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[Pw_forum] Wannier BandStructure

2014-07-23 Thread Giovanni Pizzi 
Dear Tommaso,
for Wannier90-related questions, please use the dedicated mailing list 
as explained here:
http://www.wannier.org/forum.html

For your question, I suggest that you first check the most updated 
tutorial in
http://www.wannier.org/doc/tutorial.pdf
(should be example 11) together with the example files in the examples/ 
subfolder of the Wannier90 package.
This should probably help you solving your problem (most probably you 
just defined the kpoint_path block, but did not write anything in it - 
in case of doubt, see also the very exhaustive documentation 
http://www.wannier.org/doc/user_guide.pdf).
If you still encounter problems, please post any further question on the 
Wannier mailing list.

Best,
Giovanni


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Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124



On 07/23/2014 07:18 PM, Tommaso Francese wrote:
> Dear all Wannier  Users,
>  i'm beginner with Wannier90 computational method. So, it might be a 
> stupid question, but when i try to follow the 
> http://www.wannier.org/cecam07/tutorial_cecam.pdf, i'm able to do the 
> first part (Silicon Valence Bands), until the XcrysDen file 
> generation; but the next (Valence + Conduction State), following the 
> tutorial fails, and the silicon.werr warns me as follow:
>
>  Wannier90: Execution started on 23Jul2014 at 19:08:27
>  Exiting...
>  A bandstructure plot has been requested but there is no kpoint_path block
>
> Can you help me?
>
> I added the two strings as suggested in the tutorial, but it doesn't work.
>
> Thanks in advance for every tips,
> Best,
> Tommaso.
> Universit? C? Foscari di Venezia
>
>
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[Pw_forum] PW.X WORKS ONCE AND NEXT TIME DOESN'T.. FOR THE SAME INPUT FILE..

2014-07-14 Thread Giovanni Pizzi 
Dear Siddheshwar,
it is quite improbable that this error did not occur in your first run. 
You must have changed something between the two runs (and probably 
forgotten about it).

In any case, in the input file you wrote 'ecutrho=' but did not specify 
any value. This for sure is (one of the possible) causes of the error.

Best,
Giovanni


On 07/14/2014 02:01 PM, siddheshwar chopra wrote:
> Dear Users,
> I ran the pw.x successfully using 4 processors. But again when I am 
> running the same i/p file, I am getting this error:
>
> %%
>  Error in routine  read_namelists (5010):
>   reading namelist system
>  
> %%
>
>  stopping ...
>
> ===
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 1
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===
>
> Please tell me how to resolve this issue.
>
> Regards,
>
> -- 
> *Dr. Siddheshwar chopra,*
> /M.Sc., Ph.D (Physics)
> Assistant Professor (Physics),
> /
> /Amity University, Noida, India.//
> /
>
>
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[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

2014-06-01 Thread Giovanni Pizzi 

On 1 Jun 2014, at 17:41, Paolo Giannozzi wrote:

> I am not sure that xcrysden can understand the 
> "CELL_PARAMETERS {angstrom}" card, since option
> "angstrom" was added quite recently
> 
> P.

Indeed, I also noticed that Xcrysden does not properly cope with 
"CELL_PARAMETERS angstrom" (at least the version that I have installed).

As a workaround, run the calculation just for a few seconds (e.g., creating a 
prefix.EXIT file in the same folder as the input file - where you have to 
substitute 'prefix' with the prefix you chose - that will automatically stop 
the code after the initialization part) and then open instead the output file 
with xcrysden. This should work properly in both cases (i.e., input file in 
angstrom or bohr).

Best,
Giovanni



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Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124



> On Sun, 2014-06-01 at 14:41 +0530, Surender wrote:
>> Dear QE Users,
>> I don't know whether it's an issue related to XCrysDen or something is
>> wrong wih my QE input file. Following is the first input file
>> 
>> 
>> cu.scf_bohr.in
>> 
>> 
>>calculation='scf'
>>prefix='cu',
>>pseudo_dir='./pseudo',
>>outdir='./tmp'
>> /
>> 
>>ibrav=0
>>ntyp= 1,
>>nat= 4,
>>ecutwfc= 50.0,
>>occupations='smearing',
>>smearing='methfessel-paxton',
>>degauss=0.005
>> /
>> 
>>conv_thr = 1.0D-10
>>mixing_beta = 0.7
>> /
>> ATOMIC_SPECIES
>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>> ATOMIC_POSITIONS {bohr}
>> Cu 0. 0. 0.
>> Cu 3.4155 3.4155 0.
>> Cu 0. 3.4155 3.4155
>> Cu 3.4155 0. 3.4155
>> K_POINTS automatic
>>   12 12 12 0 0 0
>> CELL_PARAMETERS {bohr}
>>   6.831 0.000 0.000
>>   0.000 6.831 0.000
>>   0.000 0.000 6.83
>> ==
>> 
>> I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I mean
>> no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
>> PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
>> structure then atoms start overlapping. Following is the second input file
>> 
>> 
>> cu.scf_angstrom.in
>> 
>> 
>>calculation='scf'
>>prefix='cu',
>>pseudo_dir='./pseudo',
>>outdir='./tmp'
>> /
>> 
>>ibrav=0
>>ntyp= 1,
>>nat= 4,
>>ecutwfc= 50.0,
>>occupations='smearing',
>>smearing='methfessel-paxton',
>>degauss=0.005
>> /
>> 
>>conv_thr = 1.0D-10
>>mixing_beta = 0.7
>> /
>> ATOMIC_SPECIES
>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>> ATOMIC_POSITIONS {angstrom}
>> Cu 0. 0. 0.
>> Cu 1.8074 1.8074 0.
>> Cu 0. 1.8074 1.8074
>> Cu 1.8074 0. 1.8074
>> K_POINTS automatic
>>   12 12 12 0 0 0
>> CELL_PARAMETERS {angstrom}
>>   3.6148 0. 0.
>>   0. 3.6148 0.
>>   0. 0. 3.6148
>> 
>> 
>> I don't know what's going on or did I miss something. I am using XCrysDen
>> Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.
>> 
>> Thanks,
>> Surender
>> IIT Bombay, India
>> 
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[Pw_forum] pw2wannier.x error

2014-05-28 Thread Giovanni Pizzi 
Dear Rajdeep,
at a quick glance everything seems ok, if you want a quantitative 
comparison you can also check the sample output files that we 
distributed with the paper: http://dx.doi.org/10.1016/j.cpc.2014.05.004 
(follow 'program summary URL', then 'download').

If you have further questions specific on Wannier90, I suggest you to 
write on the Wannier mailing list rather than here (see instructions 
here: http://www.wannier.org/forum.html )

Best,

Giovanni


On 05/27/2014 12:06 PM, Rajdeep Banerjee wrote:
> Dear Giovanni Pizzi,
>  Thank you very much for your generous 
> help. I think wannier90-2.0.0 is compatible with espresso-5.0.3. Can 
> you please check the attached input and output files 
> (Si_boltzmann.tar.gz ) to see if there's any discrepancy (as I'm just 
> a beginner in wannier )Here's a step by step list of the things I did:
> 1. downloaded "espresso+PHonon-5.0.3.tar.gz"
> 2. unpacked:  tar -zxvf espresso+PHonon-5.0.3.tar.gz
> 3. cd espresso-5.0.3
> 4. ./configure --enable-parallel
> 5. make pw
> 6. make pp
>
> I downloaded wannier90-2.0.0:
> 1. cp ./config/make.sys.gfort ./make.sys
> 2. make
>
> Then I ran the files in ./examples/example16/
>
> >> path/espresso-5.0.3/bin/pw.x < Si.scf > Si.scf.out
> >> path/espresso-5.0.3/bin/pw.x < Si.nscf > Si.nscf.out
> >> pathforwannier2.0.0/wannier90.x -pp Si
> >> path/espresso-5.0.3/bin/pw2wannier90.x < Si.pw2wan > Si.pw2wan.out
> >> pathforwannier2.0.0/wannier90.x Si
> >> pathforwannier2.0.0/postw90.x Si
>
> All these were run in serial and parallel (except of course 
> wannier90.x) without error.
>
> Thanks a lot.
>
> Rajdeep Banerjee
> JNCASR
> Bangalore, India
>
>
>
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[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

2014-05-27 Thread Giovanni Pizzi 
Dear David,
I think that the relative (crystal) coordinates that you write for the 
5-atom cell are still expressed in terms of the conventional cell (the 
one with vectors (a,0,0), (0,a,0), (0,0,c). This is the cell used in the 
case ibrav=14, reason for which you get the correct structure.

Instead, the cell used in ibrav=7 is the primitive one - the docs say:

v1=(a/2)(1,-1,c/a),  v2=(a/2)(1,1,c/a),  v3=(a/2)(-1,-1,c/a)

Therefore you have to express the relative (crystal) coordinates with 
respect to this basis set, and not in terms of the lattice vectors of 
the conventional cell.

Best,

Giovanni Pizzi



On 05/27/2014 03:48 PM, David Foster wrote:
> Dear users
>
> The atomic positions for BaNi2As2 crystal with space group of I4/mmm (139) 
> are:
>
> Ba (2a): 0, 0,   0
> As (4e): 0, 0,   0.3471
> Ni(4d):   0, 0.5, 0.25
>
> I used MS Visualizer to build the conventional tetragonal cell (a = b = 
> 4.1474  c = 11.619).
>
> After seeing the structure with MS, I convert it to primitive and finding all 
> atoms positions. Only 5 atoms there are in primitive (If I am right):
>
> Ba 0.00 0.00  0.00
> As 0.347100 0.347100  0.00
> As 0.652900 0.652900  0.00
> Ni 0.75 0.25  0.50
> Ni 0.25 0.75  0.50
>
> I prepared two input file for QE5.0.3, one with ibrav=7 and 5 atoms, and the 
> other with ibrav=14 and all atoms in conventional cell instead of its 
> primitive:
> with P1 symmetry, the cell has 10 atoms:
> Ba 0. 0.  0.
> Ba 0.5000 0.5000  0.5000
> As 0.000 0.000  0.3471
> As 0.5000 0.5000  0.8471
> As 0.000 0.000  0.6529
> As 0.5000 0.5000  0.1529
> Ni 0.000 0.5000  0.25000
> Ni 0.500 0.  0.25
> Ni 0.000 0.5000  0.75000
> Ni 0.500 0.  0.75
>
> I have attached two inputs and two pictures that xcrysden shows. While 
> ibrav=14 shows the crystal correctly, ibrav=7 has a problem and doesn't show 
> the crystal properly. I am confused!!
> Any help will be appreciated.
>
>
>
> Then, I
>   
> Regards
>
> David Foster
>
> Ph.D. Student of Chemistry
>
>
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[Pw_forum] pw2wannier.x error

2014-05-25 Thread Giovanni Pizzi 
Dear Rajdeep Banerjee,

between the different 5.0.X versions of Quantum Espresso, there have been some 
internal changes; as a consequence, the pw2wannier90.f90 file provided with the 
Wannier90 code might not work with all 5.0.X versions.

If I remember correctly, the pw2wannier90.f90 provided with Wannier90 should 
work fine with QE version 5.0.3.

However, we have also committed an updated, working version of pw2wannier90.f90 
in the SVN trunk of Quantum ESPRESSO, so if you are still experiencing problems 
you should also try to recompile the most recent SVN and see if the problem is 
solved (this is the file that is going to be released with QE 5.1, that should 
be released soon - therefore with QE 5.1, there will be no need anymore to copy 
the pw2wannier90.f90 file manually).

If, after trying with the above-mentioned versions, you still experience the 
same problems, please provide more information (pw.x input files, Si.pw2wan 
file, and maybe also the .nnkp file) so that we may try to give you more help.

Best,
Giovanni Pizzi


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Phone: +41 21 69 31124




On 25 May 2014, at 12:50, Rajdeep Banerjee wrote:

Dear all,
 I'm facing problems when running pw2wannier.x. It always shows the 
following error regardless of a serial or parallel run :

/espresso-5.0.1/bin/pw2wannier90.x < Si.pw2wan > Si.pw2wan.out
Fatal error in PMPI_Bcast: Invalid buffer pointer, error stack:
PMPI_Bcast(1478): MPI_Bcast(buf=(nil), count=1, MPI_INTEGER, root=0, 
MPI_COMM_WORLD) failed
PMPI_Bcast(1453): Null buffer pointer


For installation I followed the following instructions in
http://www.wannier.org/pwscf.html

"
v5.0 and later
You need one file: pw2wannier90.f90, which should be copied to the "PP/src" 
directory of the QE distribution, replacing the file of the same name that is 
already there. "

Then compiled using
make all

 Please help.
Thanks,
Rajdeep Banerjee
JNCASR
Bangalore, India
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[Pw_forum] Error in a vc_relax calculation

2014-03-27 Thread Giovanni Pizzi 
Dear David,
as the output says:

calculation 'vc_relax' not allowed

And indeed vc_relax is not a valid calculation type. The valid string 
you have to insert is 'vc-relax'.

Best,
Giovanni


On 03/27/2014 03:28 PM, David Foster wrote:
> Dear Users,
> I have relaxed a bulk of Pd with "calculation=relax", but I get error when I 
> change it with
>
> "calculation=vc-relax". I added the card needed to the input. I have attached 
> input and
>
> its output containing the error.
>
> It will be appreciated if anyone help.
>
>
> Regards
>
> David Foster
>
> Ph.D. Student of Chemistry
>
>
> ___
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-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] Order of Total Energy in SCF calculations

2013-12-20 Thread Giovanni Pizzi 
Dear Manu Hedge,
I don't know what you mean by "perfect", anyway it seems to be that you still 
have almost overlapping atoms?
Best,
Giovanni


On 20 Dec 2013, at 22:07, Manu Hegde wrote:

Thanks for your kind reply. Yeah I repeated this time by double checking my 
crystal coordinates with both VESTA and XRYSDYNE. It is perfect. Lorenzo, you 
are right I think. I will double check my pseudopotentials now. Then I will run 
the calcuations. Here is my new input data and outfile, still SCF energies are 
out of order!

 
 calculation = 'scf' ,
  outdir = '/home/owner/' ,
  pseudo_dir = '/host/qexpress/espresso-5.0.2/pseudo/' ,
  prefix = 'ga2o3' ,
 /
 
   ibrav = -12,
   A = 12.34 ,
   B = 3.08 ,
   C = 5.87 ,
   cosAB = 0 ,
   cosAC = -0.24 ,
   cosBC = 0 ,
 nat = 10,
ntyp = 2,
 ecutwfc = 70 ,
 ecutrho = 840 ,
   nosym = .false. ,
nbnd = 50,
  tot_charge = 0.00,
 occupations = 'smearing' ,
 degauss = 0.001 ,
exxdiv_treatment = 'gygi-baldereschi' ,
 /
 
electron_maxstep = 200,
conv_thr = 5.D-14 ,
 startingpot = 'file' ,
 startingwfc = 'atomic' ,
 mixing_mode = 'local-TF' ,
 mixing_beta = 0.4 ,
 mixing_ndim = 10,
 diagonalization = 'david' ,
 /
ATOMIC_SPECIES
   Ga   69.72300  Ga.pbe-mt_fhi.UPF
O   15.99900  O.pbe-kjpaw.UPF
ATOMIC_POSITIONS crystal
   Ga  0.091000.00.794001  0  1
   Ga  0.090000.00.795001  0  1
   Ga  0.342000.00.686001  0  1
   Ga  0.341000.00.686001  0  1
O  0.163000.00.109001  0  1
O  0.167000.00.101001  0  1
O  0.495000.00.257001  0  1
O  0.496000.00.255001  0  1
O  0.826000.00.436001  0  1
O  0.828000.00.436001  0  1
K_POINTS gamma


Output file is



 Program PWSCF v.5.0.2 (svn rev. 9392) starts on 20Dec2013 at 10:49:16

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL 
http://www.quantum-espresso.org",
 in publications or presentations arising from this work. More details at
 http://www.quantum-espresso.org/quote.php

 Serial version

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3
 Waiting for input...
 Reading input from standard input
   file Ga.pbe-mt_fhi.UPF: wavefunction(s)  4d 4f renormalized

 gamma-point specific algorithms are used

 G-vector sticks info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Sum90593023749   600859   115693   14483
 Tot45301512375



 bravais-lattice index =  -12
 lattice parameter (alat)  =  23.3192  a.u.
 unit-cell volume  =1461.5653 (a.u.)^3
 number of atoms/cell  =   10
 number of atomic types=2
 number of electrons   =48.00
 number of Kohn-Sham states=   50
 kinetic-energy cutoff =  70.  Ry
 charge density cutoff = 840.  Ry
 convergence threshold =  5.0E-14
 mixing beta   =   0.4000
 number of iterations used =   10  local-TF  mixing
 Exchange-correlation  =  SLA  PW   PBX  PBC ( 1 4 3 4 0)
 EXX-fraction  =0.00

 celldm(1)=  23.319220  celldm(2)=   0.249595  celldm(3)=   0.475689
 celldm(4)=   0.00  celldm(5)=  -0.24  celldm(6)=   0.00

 crystal axes: (cart. coord. in units of alat)
   a(1) = (   1.00   0.00   0.00 )
   a(2) = (   0.00   0.249595   0.00 )
   a(3) = (  -0.114165   0.00   0.461786 )

 reciprocal axes: (cart. coord. in units 2 pi/alat)
   b(1) = (  1.00 -0.00  0.247226 )
   b(2) = (  0.00  4.006494 -0.00 )
   b(3) = (  0.00  0.00  2.165506 )


 PseudoPot. # 1 for Ga read from file:

[Pw_forum] Getting error

2013-12-14 Thread Giovanni Pizzi 
Dear Manu Hedge,
from a first inspection to your input file:
- as the name of the variable and the documentation say, cosAB, cosAC and cosBC 
are the cosines of the angles and not the angle in degrees, and as such must be 
a number between -1 and 1
- do you really need to specify nr1, nr2, nr3, nr1s, nr2s, nr3s?

Best,
Giovanni

--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 14 Dec 2013, at 17:13, Manu Hegde wrote:

Sorry about giving less informaton. Here is my input file for monoclinic 
gallium oxide supercell. Gallium is in both Td and Oh coordinates and Oxygen is 
in three asymmetric position.

 
 calculation = 'scf' ,
  outdir = '/home/owner/' ,
  pseudo_dir = '/host/qexpress/espresso-5.0.2/pseudo/' ,
  prefix = 'galium' ,
 /
 
   ibrav = -12,
   A = 12.23 ,
   B = 3.040 ,
   C = 5.807 ,
   cosAB = 90 ,
   cosAC = 103.7 ,
   cosBC = 90 ,
 nat = 30,
ntyp = 2,
 ecutwfc = 50 ,
 ecutrho = 200 ,
   nosym = .true. ,
   nosym_evc = .true. ,
   noinv = .true. ,
no_t_rev = .true. ,
force_symmorphic = .true. ,
use_all_frac = .true. ,
nbnd = 200,
  tot_charge = 0.00,
exxdiv_treatment = 'gygi-baldereschi' ,
 nr1 = 21 ,
 nr2 = 17 ,
 nr3 = 26 ,
nr1s = 13 ,
nr2s = 14 ,
nr3s = 11 ,
 /
 
 /
ATOMIC_SPECIES
   Ga   31.0  Ga.pbe-mt_fhi.UPF
O8.0  O.pz-rrkjus.UPF
ATOMIC_POSITIONS angstrom
   Ga  0.004060.04.4736050001  0  1
   Ga  0.004063.037104.4736050001  1  1
   Ga 10.8239510000.01.1564040001  1  1
   Ga 10.8239510003.037101.1564040001  1  1
   Ga  6.111061.518554.4736050001  1  1
   Ga  4.7169510001.518551.1564040001  1  1
   Ga  1.501941.518551.7678230001  1  1
   Ga  9.3260710001.518553.8621860001  1  1
   Ga  7.6089390000.01.7678230001  0  1
   Ga  7.6089390003.037101.7678230001  1  1
   Ga  3.2190710000.03.8621860001  0  1
   Ga  3.2190710003.037103.8621860001  1  1
O  1.8570210000.00.6181750001  0  1
O  1.8570210003.037100.6181750001  1  1
O  8.9709890000.05.0118340001  0  1
O  8.9709890003.037105.0118340001  1  1
O  7.9640210001.518550.6181750001  1  1
O  2.8639890001.518555.0118340001  1  1
O  1.3360970000.03.1708210001  0  1
O  1.3360970003.037103.1708210001  1  1
O  9.4919130000.02.4591880001  0  1
O  9.4919130003.037102.4591880001  1  1
O  7.4430970001.518553.1708210001  1  1
O  3.3849140001.518552.4591880001  1  1
O 11.8094990001.518551.444661  1  1
O -0.9814880001.518554.1853490001  1  1
O  5.7024990000.01.444661  0  1
O  5.7024990003.037101.444661  1  1
O  5.1255120000.04.1853490001  0  1
O  5.1255120003.037104.1853490001  1  1
K_POINTS automatic
  2 2 2   1 1 1


Here is my output error

 Program PWSCF v.5.0.2 (svn rev. 9392) starts on 12Dec2013 at 21:26:31

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL 
http://www.quantum-espresso.org<http://www.quantum-espresso.org/>",
 in publications or presentations arising from this work. More details at
 http://www.quantum-espresso.org/quote.php

 Serial version

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3
 Waiting for input...
 Reading input from standard input
   file Ga.pbe-mt_fhi.UPF: wavefunction(s)  4d 4f renormalized
   file O.pz-rrkjus.UPF: wavefunction(s)  2S renormalized

 Atomic positions and unit cell rea

[Pw_forum] "not orthogonal operation" during vc-relax when optimizing graphene

2013-05-04 Thread Giovanni Pizzi 
Dear Peng Tao,

as Mohnish Pandey has reported, cell_dofree = 'xy' is not the right option for 
you.

In recent versions of QE (I don't know if already in 5.0.2, for sure in the SVN 
version) there is the
cell_dofree = '2Dxy'
option that allows the first two cell vectors to freely change on the plane 
(i.e. both the x and y coordinates of the first two vectors are free to move), 
that is what you want.

If you have an old version that does not accept this option, you may want to 
switch to a recent version of QE, or simply add the following lines to you 
Modules/cell_base.f90 file (and recompile)

CASE ('2Dxy')
  iforceh  = 0
  iforceh(1,1) = 1
  iforceh(2,2) = 1
  iforceh(1,2) = 1
  iforceh(2,1) = 1

(see here to discover where to put these lines:
http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse=%2Ftrunk%2Fespresso%2FModules%2Fcell_base.f90=markup
)

Best,
Giovanni Pizzi

--
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124




On 3 May 2013, at 02:26, mohnish pandey wrote:

Dear Peng,

The cell you might be using is 'hexagonal' and the 'vc-relax' that you are 
doing has two degrees of freedom in x and y direction which are orthogonal due 
the flag 'cell_dofree = xy' you set. Since the symmetry is breaking in the 
second step due to relaxation in x and y direction it is changing the number of 
k-points. That's why you are getting that error. A simple work-around for this 
is you use a bit bigger cell with orthorhombic symmetry (in which you have 
orthogonal 'a' and 'b' vectors). In orthorhombic cell symmetry won't break due 
to 'cell_dofree = xy'.


On Fri, May 3, 2013 at 4:13 AM, Peng Tao mailto:ptao10b 
at imr.ac.cn>> wrote:
Dear all,

Recently, I just want to putting 'vc-relax' to optimize the graphene structure,
but it repots an error:
%%
 from checkallsym : error # 2
 not orthogonal operation
%%

And I set 'cell_dofree = xy' in the vc-relax run.

I know, it is no need to apply vc-relax to graphene, and only relax can aquire
my result. But if I want to relax bi-layer and mutilayer graphene and my 
ultimate
goal is to get their phonon dispersion curves(so the symmetry should not be 
broken),
how could I do? Is there any convienient method to relax them?

Thanks a lot.

Yours,
Peng Tao

--
---
PH.D. candidate Peng Tao
Magnetism and Magnetic Materials Division
National Laboratory for Material Science
Institute of Metal Research, Chinese Academy of Sciences
Phone  +86-024-83978751<tel:%2B86-024-83978751>
---



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Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic Scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] phonon density of states calculation of a mono-clinic crystal

2013-02-19 Thread Giovanni Pizzi 
Dear Matthijs,

if you open the .dyn files, the third line will contain
num_species num_atoms ibrav celldm(1) celldm(2) celldm(3) celldm(4) 
celldm(5) celldm(6)
and as you can see celldm(1) is set to zero. You have to set it to the 
correct value taken from your pw.x output.

The best thing though is that you reinstall a more recent version of QE, 
where this and a few other bugs have been corrected.

Giovanni


On 02/19/2013 05:53 AM, Matthijs Mentink wrote:
> Thank you for your quick responses.
>
> After noting that I had made an unrelated mistake somewhere, which 
> means recalculation was inevitable, I have decided to simply define 
> the crystal as mono-clinic (using ibrav = 12) and to recalculate.
>
> I've included the pwscf input file and two dyn files that resulted in 
> the error message. The version I'm using is espresso 5.0.0.
>
> Thanks again for your assistance.
>
> Matthias Mentink
> PhD candidate
> Superconducting magnet group,
> Lawrence Berkeley National Laboratory,
> Berkeley, CA
>
>
> On Thu, Feb 14, 2013 at 1:55 AM, Paolo Giannozzi 
> mailto:giannozz at democritos.it>> wrote:
>
> On Thu, 2013-02-14 at 10:35 +0100, Giovanni Pizzi wrote:
>
> > I think it should be possible to fix the problem directly in the
> > matdyn files, without rerunning pw and ph.
>
> for sure it is not needed to re-run the entire calculation,
> but it may be needed to comment out some overzealous check
> from q2r.f90 or related routines
>
> P.
>
> > On 02/14/2013 12:40 AM, Matthijs Mentink wrote:
> >
> > > Dear all,
> > >
> > > I'm trying to calculate the phonon density of states as a function
> > > of energy of a mono-clinic crystal. I use ibrav = 0 and define
> > > lattice vectors using 'CELL_PARAMETERS {bohr]'.
> > >
> > > This allows me to do a self-consistent calculation (pw.x) and
> phonon
> > > dispersion calculations (ph.x) but I run into trouble when I
> try to
> > > use q2r.x. This is the error message that I get:
> > >
> > > Error in routine read_file (1):
> > >  wrong celldm
> > >
>
> > >
> > > In the pwscf input file I don't define celldm, because I use
> ibrav =
> > > 0, but q2r seems to have a problem with that.
> > >
> > > Is there any way to fix this? Would it work if I start from
> scratch
> > > (not a very appealing option) and use ibrav = 12?
> > >
> > > thanks in advance,
> > >
> > > Matthias Mentink
> > > PhD candidate
> > > Superconducting magnet group,
> > > Lawrence Berkeley National Laboratory,
> > > Berkeley, CA
> > >
> > >
> > > ___
> > > Pw_forum mailing list
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> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> >
> > --
> > Giovanni Pizzi
> > Post-doctoral Research Scientist
> > EPFL STI IMX THEOS
> > MXC 340 (B?timent MXC)
> > Station 12
> > CH-1015 Lausanne (Switzerland)
> > Phone: +41 21 69 31124 <tel:%2B41%2021%2069%2031124>
> > ___
> > Pw_forum mailing list
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> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> ___
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>
>
>
>
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-- 
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MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] phonon density of states calculation of a mono-clinic crystal

2013-02-14 Thread Giovanni Pizzi 
Hi,
there was such a problem in earlier versions but it should have been 
fixed in recent ones. Which version of quantum espresso are you using?

Could you also post the first few lines of your prefix-matdyn1 file, and 
your pw and ph input/output files? For the future it is better to run 
with new versions, but I think it should be possible to fix the problem 
directly in the matdyn files, without rerunning pw and ph.

Best,
Giovanni Pizzi


On 02/14/2013 12:40 AM, Matthijs Mentink wrote:
> Dear all,
>
> I'm trying to calculate the phonon density of states as a function of 
> energy of a mono-clinic crystal. I use ibrav = 0 and define lattice 
> vectors using 'CELL_PARAMETERS {bohr]'.
>
> This allows me to do a self-consistent calculation (pw.x) and phonon 
> dispersion calculations (ph.x) but I run into trouble when I try to 
> use q2r.x. This is the error message that I get:
>
> /Error in routine read_file (1):
>  wrong celldm/
>
> In the pwscf input file I don't define celldm, because I use ibrav = 
> 0, but q2r seems to have a problem with that.
>
> Is there any way to fix this? Would it work if I start from scratch 
> (not a very appealing option) and use ibrav = 12?
>
> thanks in advance,
>
> Matthias Mentink
> PhD candidate
> Superconducting magnet group,
> Lawrence Berkeley National Laboratory,
> Berkeley, CA
>
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] question on parallelism options and scaling factor

2013-02-06 Thread Giovanni Pizzi 
Dear Pascal,
since you have more than one k-point, you could try to have each pool 
within one node, so that only inter-pool communication occurs over 
infiniband; for instance if you have 4 k-points you may try to use 4 
pools on 4 nodes (or possibly 2 pools on 2 nodes, or 4 pools on 2 nodes, 
etc).
This kind of parallelization should scale pretty well, if your system 
allows it (i.e. you have  enough kpoints and your system fits in RAM). 
Then, you can try to optimize the parallelization using the other 
parallelization options.

If you manage to do some scaling tests using the pools, could you please 
report your results on this mailing list?

Thanks, and best regards,

Giovanni Pizzi


On 02/05/2013 10:12 PM, pascal boulet wrote:
> Dear all,
>
> I have a basic question about parallelism and scaling factor.
>
> First, I am running calculations on a cubic system with 58 atoms
> (alat=19.5652  a.u.), 540 electrons (324 KS states) and few k-points
> (4x4x4 grid=4 k-points), on 32 cores (4 nodes) but I can submit on many
> more.
>
> I guess the best thing to do is to parallelize the calculation on the
> bands but maybe also on the FFTs. We have an infiniband interconnection
> network between the nodes.
>
> What would you suggest as values for image/pools/ntg/bands ?
>
> I have made a SCF test calculation on 16 and 32 cores. For the SCF cycle
> (13 steps) I get the following timing:
> For 16 cores: total cpu time spent up to now is22362.4 secs
> For 32 cores: total cpu time spent up to now is17932.6 secs
>
> The speedup is "only" 25%. I would have expected a better speedup for
> such a small number of cores. Am i wrong? What is your experience?
>
> (For additional information, if helpful: QE 5.0.1 has been compiled with
> openMPI, intel 12.1 and FFTW 3.2.2.)
>
> thank you for your answers.
>
> Regards
> Pascal
>
>
>
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EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124

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[Pw_forum] error in find_mode_sym.f90

2013-01-29 Thread Giovanni Pizzi 
Dear Bramha,
as Andrea Dal Corso already pointed out, this may be due to 
incompatibilities with the linking to the blas libraries. It appears 
that you are using your system-provided blas and lapack libraries.

As Andrea said, try to reconfigure quantum espresso adding the
--with-internal-blas --with-internal-lapack
flags to the ./configure and then recompile everything to see if the 
problem disappears.

In fact, there is a known incompatibility problem between the calling 
convention for functions that return complex values: one is the one used 
by g77/f2c, where in practice the compiler converts such functions to 
subroutines with a further parameter for the return value; gfortran 
instead produces a normal function returning a value (and maybe also 
ifort?). If your system libraries were compiled using g77, and you 
instead use gfortran (or possibly ifort?) your code may crash or produce 
random results. This typically happens with zdotc, which is one the most 
commonly used complex-returning functions in blas+lapack.

For further details see for instance this link:
http://www.macresearch.org/lapackblas-fortran-106#comment-17071

Otherwise, another trick that you can try if you use gfortran and you 
confirm that this is the problem, is to add the -ff2c flag to all 
compilations with gfortran. But the best probably is to use libraries 
compiled with the same compiler, or at least libraries that are verified 
to work with your compiler (in your case, since it appears that you use 
ifort, you may want to link to the proper intel MKL libraries).

Best,

Giovanni Pizzi


On 01/29/2013 11:48 AM, Bramha Pandey wrote:
> Dear Sir,
> I am sending my make.sys file to you. Due to executable file i have 
> change it name make only.
> Please find the attachment.
> I am very grateful for your kind help.
>
> On Tue, Jan 29, 2013 at 2:43 PM, Andrea Dal Corso  <mailto:dalcorso at sissa.it>> wrote:
>
>
> On Tue, 2013-01-29 at 13:57 +0530, Bramha Pandey wrote:
> > Dear Prof. Paolo,
> > Thanks for your kind reply.
> > As per my search, i got the same error with svn espresso (version
> > PHONON v.5.0.2 (svn rev. 9881)) and by espresso-5.0.2 (PHONON
> v.5.0.2
> > (svn rev. 9392)) to run the examples01 and example02.
> > By seeing the out put of ph.x only prints
> > There are   3 irreducible representations
> >
> >  Representation 1  2 modes -  To be done
> >
> >  Representation 2  2 modes -  To be done
> >
> >  Representation 3  2 modes -  To be done
> >
> >
> >
> >  Alpha used in Ewald sum =   0.7000
> >  PHONON   : 1.92s CPU 2.35s WALL
> >
> >
> >
> >  Representation #  1 modes #   1  2
> >
> >  Self-consistent Calculation
> >
> > after that at terminal the following error messages are appeared.
> >
> >  running the scf calculation for Si... done
> >   running the phonon calculation at Gamma for Si...forrtl: severe
> > (174): SIGSEGV, segmentation fault occurred
> > Image  PCRoutineLine
> > Source
> > ph.x   08076447  find_mode_sym_new   145
> > find_mode_sym.f90
> > ph.x   08151582  set_irr_new_  158
> > set_irr.f90
> > ph.x   0813D510  find_irrep_32
> > find_irrep.f90
> > ph.x   0807AB66  init_representati   103
> > init_representations.f90
> > ph.x   0804E7FF  check_initial_sta   161
> > check_initial_status.f90
> > ph.x   0804B531  MAIN__   91  phonon.f90
> > ph.x   0804B484  Unknown Unknown  Unknown
> > libc.so.6  B68374D3  Unknown Unknown  Unknown
> >  done
> >   running the phonon calculation at X for Si...forrtl: severe (174):
> > SIGSEGV, segmentation fault occurred
> >
> > Stack trace terminated abnormally.
> > Error condition encountered during test: exit status = 174
> > Aborting
> >
> > As per my knowledge the error is coming at 145 lines in
> > 'find_mode_sym.f90 which is DO i=1,dim_rap(igroup).
> > Dear Sir now i am further helpless why this is occured as if i
> > compared with espresso-4.3.2(which runs without any problem)
> this line
> > is written as DO i=1,dim_rap.
> >
>
> Please provide your make.sys, or try to link with the internal
> blas and
> lapack libraries. I do not know if this apply to your case, but I have
> seen an error

[Pw_forum] ph.x: Wrong classes for C_3v

2013-01-16 Thread Giovanni Pizzi 
Dear David,
more interestingly, already the scf calculation crashes if the flag
verbosity='high'
is set, to print (among other stuff) the symmetry information.

Is there a specific reason for which your v1 cell vector has one more 
significant digit (5.427632) w.r.t. v2 and v3?
In your specific case, setting v1_x to 5.42763 should solve the problem.

But I agree that probably it is worth trying to go into the code to try to 
avoid the occurrence of such kind of errors.

Best,
Giovanni




On 16 Jan 2013, at 12:10 AM, David Strubbe wrote:

Dear QE developers,

I have encountered an internal error regarding symmetry with QE 5.0.2, for a 
calculation with 8 atoms of Si. The scf calculation with pw.x runs fine, but 
then ph.x crashes immediately with the following message. This happened in 
serial and parallel with ifort, as well as in serial with gfortran. Input files 
scf.in and ph.in are below also. I tried with 
the patch to 5.0.3 emailed out by Dr. Gianozzi a few weeks, and got the same 
error.

David Strubbe
MIT

 %%
 Error in routine divide_class (1):
 Wrong classes for C_3v
 %%

$ cat scf.in

   prefix = 'silicon'
   calculation = 'scf'
   restart_mode = 'from_scratch'
   pseudo_dir = '/home/dstrubbe/raman_Si/pseudo'
/

   ibrav = 0
   celldm(1) = 1.88972613
   nat = 8
   ntyp = 1
   nbnd = 32
   ecutwfc = 50.0
/

/
CELL_PARAMETERS
5.427632 0.0 0.0
0.0 5.42763 0.0
0.0 0.0 5.42763
ATOMIC_SPECIES
  Si  28.086  Si.UPF
ATOMIC_POSITIONS angstrom
Si 0.5427630.5427630.542763
Si 3.2565793.2565790.542763
Si 0.5427633.2565793.256579
Si 3.2565790.5427633.256579
Si 1.8996711.8996711.899671
Si 4.6134874.6134871.899671
Si 1.8996714.6134874.613487
Si 4.6134871.8996714.613487
K_POINTS automatic
1 1 1 0 0 0

$ cat ph.in
phonons of Si at Gamma
 
  tr2_ph=1.0d-12,
  prefix='silicon',
  epsil=.true.,
  trans=.true.,
  amass(1)=28.0855,
 /
0.0 0.0 0.0

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[Pw_forum] plotrho.x

2012-11-26 Thread Giovanni Pizzi 
Dear Sakhraoui,
try to run the plotrho.x program interactively and type in manually the 
values, instead of providing an input file.
In this way, you will see what the code is asking for.

In your case, apparently the last line should be a file name, while you 
are providing

0 0.09 10,


Best,
Giovanni Pizzi

-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159



On 11/26/2012 04:12 PM, Sakhrawi Taoufek wrote:
> Dear all,
> i want to run plotrho.x for FeRh,
> my input file
> ###
>   ferh_fm.charge001.dat
>  0. 0. 0.,
>  0. 0. 1.,
>  1. 1. 0.,
>   ferh_fm.charge001.ps
>  29  41 ,
>  n
>  0.001411 0.087060,
>  0 0.09 10,
> ###
> the error message :
> "At line 40 of file plotrho.f90 (unit = 1, file = '')
> Fortran runtime error: File '
>  0 0.09 10,' does not exist"
> i read the file  "plotrho.f90"but i can't understand where is the problem
> There is any idea??
> any suggestion will be appracieted
> thanks
> 
> Sakhraoui Taoufik
> Ph.D student
> Faculty of Sciences of Monastir
> Department of Physics
> L.M.C.N
> Monastir, Tunisia
> 
>
>
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[Pw_forum] Relaxtion

2012-11-06 Thread Giovanni Pizzi 
Dear Sakhrawi,
try also to put the  namelist before ions and cell. This 
should solve the problem.

Note also that in the K_POINTS card you probably want to specify
10 10 10 1 1 1
rather than
10 10 10 1

Best,
Giovanni Pizzi

-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159


On 11/05/2012 08:49 PM, Lorenzo Paulatto wrote:
>
>
> On 1 November 2012 16:36, Sakhrawi Taoufek  <mailto:tsakhrawi at yahoo.com>> wrote:
>
> %%%
>  from  read_namelists  : error # 1
>   reading namelist ions
>  %%
>
>
>
> Dear Sakhrawi,
> everything seems to be ok, maybe there is some strange character in 
> your input (you can check with "cat -v input.file" and see if anything 
> strange appears).
>
> In a desperate case, you may try to invert the order of the namelists 
>  and , with some compiler one of the two orders is not good, 
> but I do not remember which.
>
> good luck
>
> -- 
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www: http://www-int.impmc.upmc.fr/~paulatto/ 
> <http://www-int.impmc.upmc.fr/%7Epaulatto/>
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
>
>
>
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[Pw_forum] CrayXE6

2012-09-20 Thread Giovanni Pizzi 
Dear Sam,
You may want to take a look to the instructions to compile on the rosa machine 
at CSCS, Switzerland, which is a CrayXE6 (with the PGI compiler, though) 
provided by Filippo Spiga and that you can find here:

http://qe-forge.org/gf/project/q-e/scmsvn/?action=browse=%2Ftrunk%2Fespresso%2Finstall%2FREADME.CSCS_rosa=markup

Best,
-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159



On 20 Sep 2012, at 6:35 PM, Sam Azadi wrote:

> Dear PWSCF developers,
> 
> Stuck in compiling on  CrayXE6 machines,
> using "ftn" wrapper, GNU compiler suits "PrgEnv-gnu", and "acml" libraries.
> Really appreciate any comment/example/experience ...
> 
> Yours
> Sam
> 
> -- 
> ***
> Sam Azadi
> Institute of Physical Chemistry and
> Center for Computational Sciences
> Johannes Gutenberg University Mainz
> Staudinger Weg 9, D-55128 Mainz,Germany
> Tel: +49 6131 3926844
> ***
> 
> ___
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> http://www.democritos.it/mailman/listinfo/pw_forum

[Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm

2012-08-22 Thread Giovanni Pizzi 
On 08/22/2012 03:40 PM, Paolo Giannozzi wrote:
> I think that variable celldm should disappear ... Thank you anyway for 
> the report

Ok. But then, to fix the problem, one should define celldm(1) in pw.x as 
I was suggesting, or change q2r.x so that it doesn't use celldm?
Best,
Giovanni

[Pw_forum] Bug in QE 5.0 with ibrav=0 and using a instead of celldm

2012-08-22 Thread Giovanni Pizzi 
Dear all,
I believe there is a bug in QE 5.0 (pw.x) that occurs when using ibrav=0 
and defining 'a' instead of 'celldm(1)'.
In this case, celldm is not set and remains equal to zero. (This 
behavior was different in 4.3.2, where instead the celldm(1) value was 
set from the 'a' value.)

This doesn't seem to create problems in the pw.x calculation.
However, in the matdyn files generated by ph.x, the celldm(1) is set to 
zero.
When the matdyn files are then given to q2r.x, the code crashes, 
complaining of a wrong celldm value.

In particular this is what happens in q2r.x:
1. the first q point is read (matdyn1) using the routine 
read_dyn_from_file; celldm(1) is set to 0
2. the code calls the routine latgen: this routine sets celldm(1) to the 
a value different from zero (moreover this value may be wrong if 'a' in 
the input file was not set to the length of the first lattice vector)
3. the code reads the second q point (matdyn2) and compares the celldm 
value read from file (which is zero) with the old value (which was set 
to a value different from zero at step 2): being different, the code stops.

I think that to correct it, one should replace the following lines 
(cell_base.f90, lines 152 and following)
  IF( celldm( 1 ) /= 0.0_DP ) THEN
 alat = celldm( 1 )
  ELSE IF ( a /= 0.0_dp ) THEN
 alat = a / bohr_radius_angs
  ELSE
 alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 )
  END IF
  at(:,:) = at(:,:) / alat

with
  IF( celldm( 1 ) /= 0.0_DP ) THEN
 alat = celldm( 1 )
  ELSE IF ( a /= 0.0_dp ) THEN
 alat = a / bohr_radius_angs
 celldm( 1 ) = alat
  ELSE
 alat = SQRT ( at(1,1)**2+at(2,1)**2+at(3,1)**2 )
 celldm( 1 ) = alat
  END IF
  at(:,:) = at(:,:) / alat

Let me know what you think.

Best,
Giovanni Pizzi



-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159

[Pw_forum] unexpected force_symmorphic behavior with explicit k grid

2012-06-21 Thread Giovanni Pizzi 
Dear Paolo,
thanks for your answer.
Indeed, I am using Yambo which requires that flag.

The point is that Andrea Marini and I are working on a Wannier90 
interface for Yambo.
While for the generation of the automatic grids the increased number of 
k points is perfectly ok, the problem arises when we have to generate 
the full k grid that is needed by Wannier90.
In this case, in fact, if for instance I specify the 64 k points for a 
4x4x4 grid in the nscf calculation, and I leave the force_symmorphic 
flag set to true, QE will calculate the band energies on 136 k points 
instead.
Of course for this nscf calculation I can simply remove the 
force_symmorphic flag, I was just wondering if it could make more sense 
not to increase the number of k points if they are given as an explicit 
list (but maybe there are cases for which instead this is the intended 
behavior).

Giovanni


On 06/20/2012 06:27 PM, Paolo Giannozzi wrote:
> On Wed, 2012-06-20 at 17:46 +0200, Giovanni Pizzi wrote:
>> >  I was using the force_symmorphic flag of pw.x.
> you shouldn't, unless you have a good reason to use it
>
>> >  I noticed that even when I provide an explicit list of k points
>> >  (e.g. with
>> >  K_POINTS crystal
>> >  or even
>> >  K_POINTS crystal_b
>> >  for a band structure) pw.x increases the number of k points.
> "force_symmorphic" just removes the symmetry operations having
> an associated fractional translation from the list of allowed
> symmetries. Any change in the number of k-points, if any, is
> a consequence of the reduced symmetry of the system.
>
>> >  Is this the intended behavior, or should the list of K points be
>> >  modified only for K_POINTS automatic?
> hard to say what the "intended" behavior is: there isn't any.
> That option was added (by me) in order to allow PWscf to produce
> data for other codes (don;t remember which ones) that do not
> implement nonsymmorphic symmetry groups.
>
> P.
> -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy


-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159

[Pw_forum] unexpected force_symmorphic behavior with explicit k grid

2012-06-20 Thread Giovanni Pizzi 
Dear QE developers,
I was using the force_symmorphic flag of pw.x.

I noticed that even when I provide an explicit list of k points (e.g. with
K_POINTS crystal
or even
K_POINTS crystal_b
for a band structure) pw.x increases the number of k points.

Example: I want to plot the bands on a line and I use
K_POINTS {crystal_b}
2
0. 0. 0. 50.
0.5 -0.5  0. 50.

With force_symmorphic=.false. I get 51 K-points as expected;
with force_symmorphic=.true. I get instead 100 K-points (from Gamma to 
(1/2,-1/2,0) and then back again from Gamma to (-1,-1/2,-1/2) without 
the start and end point).

Is this the intended behavior, or should the list of K points be 
modified only for K_POINTS automatic?

Cheers,
Giovanni Pizzi

-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 319 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31159