Re: [Wien] Berrypi Error

; To: A Mailing list for WIEN2k users > Subject: Re: [Wien] Berrypi Error > > Caution: External email. > > > Dear Sharbano, > > Many thanks for sharing the fix. I will take a closer look in the next couple > of > days. > > Best regards > Oleg >

Re: [Wien] Berrypi Error

Dear Sharbano, Many thanks for sharing the fix. I will take a closer look in the next couple of days. Best regards Oleg > -Original Message- > From: Wien On Behalf Of > shahrbano rahimi > Sent: Friday, November 17, 2023 11:17 AM > To: A Mailing list for WIEN2k users &

[Wien] Berrypi Error

Dear Prof. Peter Blaha and Prof. Oleg Rubel, hope this email finds you in good health and spirits. I am reaching out to respectfully report a technical challenge we recently encountered in our Wien2k calculations using BerrypI, and to share the solution we found in hopes that it might be helpful.

Re: [Wien] Berrypi & w2w

t 24, 2020 16:17 To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Berrypi & w2w Technically, it should work even with 1x1x1 mesh. The loop is closed in k space through periodic boundary conditions. For a surface, x1 mesh in the perpendicular direction should be suf

Re: [Wien] Berrypi & w2w

, August 24, 2020 14:47 To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Berrypi & w2w I'd guess that for an insulator this is not a problem. It would be problematic for metals, but berrypi is not for metals anyway. Am 24.08.2020 um 19:52 schrieb Laurence Marks: > Does anyone know if

Re: [Wien] Berrypi & w2w

I'd guess that for an insulator this is not a problem. It would be problematic for metals, but berrypi is not for metals anyway. Am 24.08.2020 um 19:52 schrieb Laurence Marks: Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will happen with a surface calculation where along the

[Wien] Berrypi & w2w

Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will happen with a surface calculation where along the long direction there is only one k-point? -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu

Re: [Wien] BerryPI

Thank you very much Oleg, it worked as berrypi "-k 4:4:2" -o -p. Best regards Ali -Original Message- From: Wien [mailto:wien-boun...@zeus.theochem.tuwien.ac.at] On Behalf Of Oleg Rubel Sent: Thursday, 7 May 2020 22:15 To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Berry

Re: [Wien] BerryPI

Hi Ali, the field 'k4:4:2' is probably ignored, and the code takes a default mesh 10x10x10. I suspect it is the missing dash '-'. The execution should be 'berrypi -k 4:4:2 ...' I hope it will help Oleg -- Oleg Rubel (PhD, PEng) Department of Materials Science and Engineering McMaster

[Wien] BerryPI

Dear Users of Wien2K I am trying to use BerryPI to calculate the polarization of the LuScFeO3 structure, considering spin polarization (AFM) and LDA+U, the lattice is hexagonal (P31m) with 14 atoms per unit cell (I already got convergence in energy and charge in scf). My problem is the number

Re: [Wien] BerryPI

Dear Gavin, Yes, alias berrypi calls berrypi alias berrypi='/usr/bin/python2.7 /home/kcbhamu/Wien2k_18/SRC_BerryPI/BerryPI/berrypi' also, berrypi -h worked. thanks and regards Bhamu On Mon, Oct 1, 2018 at 5:42 PM Gavin Abo wrote: > "which berrypi" returning nothing I believe is fine since it

Re: [Wien] BerryPI

"which berrypi" returning nothing I believe is fine since it uses an alias instead. Maybe check if the berrypi alias is setup with the terminal command: alias berrypi Maybe check that you can call berrypi, for example its help with the terminal command: berrypi -h In WIEN2k 18.2, I think

[Wien] BerryPI

Dear Prof. Oleg, I just installed the Wien2k_18.2. I saw one of your reply [1] where you call BerriPI with "which": when I do the same, I am not getting anything. My python variables in 'usr/bin' are: python python2 python2.7 python3python3.6 python3.6m python3m

Re: [Wien] BerryPi

Yes, the WIEN2k limitations page [ http://susi.theochem.tuwien.ac.at/reg_user/limitations/ ] lists that the optic package doesn't work with RLOs. On 10/27/2017 8:45 AM, Dr. K. C. Bhamu wrote: Hii, I saw it but is is not helpful. Out procedure differs in many ways. Here the person is doing

Re: [Wien] BerryPi

Hii, I saw it but is is not helpful. Out procedure differs in many ways. Here the person is doing -sp+-so for Pt and he is not adding RLOs, using TETRA 0.000, and taking plasma frequency as such from outputjoint file while I am using RLO for Pb, TETRA 101 and sqrt(2)(w_pl). I do not know if I

Re: [Wien] BerryPi

Dear Dr. Bhamu In this tutorial video for optical properties with so coupling, they are using x kgen with so symmetry. So I think we should use -so tag. https://www.youtube.com/watch?v=lDW7cy1oZR4=147s Check page no 135 of the UG to know about changing tetra. Regards Lokanath

Re: [Wien] BerryPi

Dear Lokanath, Happy Diwali! Hope you are enjoying your research at CU, TU. I am having same structure what you have in recent past. https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16508.html I have three queries and looking forward your favor. *My first query:* I am not

Re: [Wien] berrypi missing -c case (in automatic)

You are right, I missed that. --- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Partner of the CFW 100% gender equity

Re: [Wien] berrypi missing -c case (in automatic)

The necessity for the ‘-c’ option is not obvious. Would you please give a hint? BerryPI executes ‘x lapw1’ and then ‘x w2w’. I both cases, ‘x’ script is used that identifies complex calculation. There is no need to be more specific and call for ‘x lapw1 -c’ or ‘x w2w -c’ (please correct me, if

[Wien] berrypi missing -c case (in automatic)

berrypi seems to need a "-c" option for the complex case, presumably can be hacked around. Similarly needed for the call of w2w that it makes (I think). -- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi

[Wien] BerryPI update

Dear wien2k Users, I just discovered a bug in BerryPI that could affect calculations of the ionic charge and ionic polarization. The symptoms are appearance of a wrong valence charge in the table of ionic polarization. CALCULATION OF IONIC POLARIZATION

Re: [Wien] BerryPi

Dear Oleg, Thanks a lot. I can find my mistake now. I will try for an insulator. On Mon, Feb 1, 2016 at 6:17 AM, Oleg Rubel wrote: > Well, the fractional occupancies indicate that this is a metal. I afraid > you cannot proceed with he effective charge calculation. BerryPI

Re: [Wien] BerryPi

Well, the fractional occupancies indicate that this is a metal. I afraid you cannot proceed with he effective charge calculation. BerryPI implies the presence of a band gap. > So if i have understood you, I have to rerun init_lapw after the displacement. Not quite, you need to change the order

Re: [Wien] BerryPi

Dear Oleg, Here I am listing the result :BAN00034: 340.2210690.307010 1. :BAN00035: 350.2463190.307010 1. :BAN00036: 360.2688320.335387 1. :BAN00037: 370.2843330.339720 1. :BAN00038: 380.3035260.345742 1.

Re: [Wien] BerryPi

87 Dresden Von: wien-boun...@zeus.theochem.tuwien.ac.at [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von lokanath patra [lokanath.patra...@gmail.com] Gesendet: Freitag, 29. Januar 2016 08:39 An: A Mailing list for WIEN2k users Betreff: Re: [Wien] BerryPi I just followed th

Re: [Wien] BerryPi

What you need it to shift both position i.e. 0.5 to 0.501 and 0. to 0.0010. Problem will be solved. regards *Dr. K. C. Bhamu(UGC-Dr. D. S. Kothari Postdoc Fellow)Department of PhysicsGoa University, Goa-403 206IndiaMob.

Re: [Wien] BerryPi

Dear Fecher and Bhamu, I also think that the error is due to the symmetry after changing the struct file. But the tutorial says ''Do not rerun the init_lapw as it may realize a higher symmetry. The intention is to keep symmetry unchanged between subsequent runs''. Just check the 3rd and 4 points

Re: [Wien] BerryPi

Hello Lokanath I did a mistake in my previous mail regarding rmt issue. Your RMT is ok (I did a mistack in compilation). your *x nn* gives error so definitely something is wrong with struct file. *Experts may help you.* regards Bhamu On Fri, Jan 29, 2016 at 11:19 AM, lokanath patra <

Re: [Wien] BerryPi

Just a small addition: It is a “must" to start with the least symmetric structure first. This implies that you need to introduce displacements, init_lapw, run(sp)_lapw, berrypy and then bring atoms back to the high symmetry position, dstart (-up/-dn), run(sp)_lapw, berrypi. In your structure

Re: [Wien] BerryPi

Dear Lokanath Your error is wellknown if you search mailing list. You may try : https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08405.html Some time ago I got same error and by compiling SRC_hf agin I overcome the error. regards

Re: [Wien] BerryPi

I just followed the tutorial of Born effective charge. According to that, we have to initialize the calculation for the unchanged material. Then we have to change the position and den we have to initialize the electron density only i.e. ''x dstart''. They have mentioned not to rerun init_lapw . So

Re: [Wien] BerryPi

One more thing: I dont know how to calculate born effective charge. But you see your new struct file there are 6 position for Bi, 6 position for O and 2 for Fe. So new composition is 3:1:3 while in original it is 1:1:3. So look on the new struct file, how you changing position of Bi and why rmt

Re: [Wien] BerryPi

Did you see any error in x nn? I am getting nn error in your Bi-changed structure, see below: Commandline: *x nn * Program input is: *"2 "* specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about 1.d-5, 20)] DSTMAX: 29.087375730 iix,iiy,iiz 5

Re: [Wien] BerryPi

Would it be possible to attach the structure files used in “initial” calculation and after the displacement is introduced? Thank you Oleg > On Jan 28, 2016, at 11:08, Dr. K. C. Bhamu wrote: > > Dear Lokanath > > Your error is wellknown if you search mailing list. > You

[Wien] BerryPi

Dear Users, I am trying to calculate born effective charge for Bi atom in BiFeO3. I followed the tutorial for GaAs as BiFeO3 is having non orthogonal lattice vectors. I used berrypi with -s option as it consists of magnetic ion. But after changing the position of Bi atom by 0.001, when I put the

Re: [Wien] BerryPI

The GGA+U calculation is likely affected by pi wrapping (-pi = +pi). So -p +(-pi) = -2*pi can be different from what you expect -pi + pi = 0. Also, I would not make conclusions based on a single calculation of polarization for a structure. All observables (spontaneous polarization, effective

[Wien] berrypi error.

Dear all I am working on the berryPI code and I have faced the following error. Can anyone help me please? Thank you in advance. Traceback (most recent call last): File "/cluster/home/lokanath/lib/w215/SRC_BerryPI/BerryPI/berrypi", line 20, in import numpy # math library File

Re: [Wien] berrypi error.

It can be related to python/numpy installation or compatibility issues. BerryPi dependencies: WIEN2k (tested against 14.2 Release 15/10/2014) WIEN2WANNIER (part of the Wien2k distribution) Python (tested against 2.7.4) NumPy (tested against 1.6.2 & 1.9.2) My suggestion would be to recreate the

[Wien] BerryPI

Dear all I have studied the polarization of some metal and insulator cases using the latest version of the berryPI code. We performed the scf calculations by Wien2k14.2. One of Our calculations for one of my cases using GGA method show that this case is an insulator in agreement with

Re: [Wien] berryPI

On 10/19/2015 10:47 AM, Peter Blaha wrote: > I'm not fully familiar with the w2wannier flow, but I can see from the > def file, that the $file.vector file already has a $hf option. Yes, I put that in “for completeness”, but it is so far completely untested. > However, then it should probably be

Re: [Wien] berryPI

The correct energy line should be: ‘$file.energy$sc$hf$soupdn’? I'll fix this in my x_lapw script for the next release. And prepare_w2wdir should take $file.scf or $file.scf2$hf$updn (not just $file.scf2$updn) And in addition, it should accpt a -hf switch and set hf=hf Peter On

Re: [Wien] berryPI

I'm not fully familiar with the w2wannier flow, but I can see from the def file, that the $file.vector file already has a $hf option. However, then it should probably be also in the $file.energy$hf line and I also see a required $file.fermi file (I don't know when it is created), but that

Re: [Wien] berryPI

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nilofar, Oleg, and Peter, I cannot say for sure whether w2w will work with HF because I have never tried it, and do not know too much about how an HF calculation works in Wien2k. If, as Peter says On 10/15/2015 09:30 PM, Peter Blaha wrote: > I

Re: [Wien] berryPI

I am really grateful for your reply and help. To my knowledge according to the w2w UG all the files constructed via WIEN2k calculations are necessary for w2w. since the flow of onsite hybrid functional is similar to the flow of LDA+U method and the switch related to the LDA+U is -o, should I

Re: [Wien] berryPI

I can confirm that case.vectorhf has the same structure than case.vertor. For testing one could simply copy case.vectorhf case.vector and try it out. I don't know if there are any other input files requires for w2w or BerryPI (case.energy ? there is also a hf file), ... Regards Am

Re: [Wien] berryPI

Perhaps other users, who are more experienced with hybrid functions and wien2wannier can add a comment. There are two hypes of hybrids: onsite and full (Sec. 4.5.7 and 4.5.8 of the UG). From BerryPI perspective, you can probably do the onsite hybrid functional the same way as the orbital

[Wien] berryPI

Dear all, I am wondering whether I am allowed to use BerryPI code for the calculations done by hybrid functional(specially B3LYP and B3PW91) or not and if it is going to what the suitable switch is! Would you please help me?! Best regards, ___ Wien

Re: [Wien] berryPI

=== >>> Dr. Gerhard H. Fecher >>> Institut of Inorganic and Analytical Chemistry >>> Johannes Gutenberg - University >>> 55099 Mainz >>> and >>> Max Planck Institute for Chemical Physics of Solids >>> 01187 Dresden >>>

Re: [Wien] berryPI

esendet: Dienstag, 8. September 2015 23:06 An: A Mailing list for WIEN2k users Betreff: Re: [Wien] berryPI I would like to add that EuTiO3 seems to be a multiferroic compound with ground state being antiferromagnetic- paraelectric system (I4/mcm). Then, under some compressive or tensile epitaxial s

Re: [Wien] berryPI code

On 09/08/2015 11:57 PM, nilofar hadaeghi wrote: > I tried to implement this run this command :x w2w -up -so > but I again faced the following error: > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PCRoutineLine > Source

Re: [Wien] berryPI code

Dear prof. Oleg Rubel and Mr.Elias Assmann I really thank You. I will try to find these lines in the source code of w2w but any further help would be desirable. BerryPI Version 1.2 Python version: 2.7.3 Numpy version: 1.6.2 Best regards, On Wed, Sep 9, 2015 at 7:45 AM, Elias Assmann

Re: [Wien] berryPI

med [sahm...@lakeheadu.ca] > Gesendet: Dienstag, 8. September 2015 23:06 > An: A Mailing list for WIEN2k users > Betreff: Re: [Wien] berryPI > > I would like to add that EuTiO3 seems to be a multiferroic compound with > ground state being antiferromagnetic- paraelectric system (I

Re: [Wien] berryPI code

My guess is that the problem is coming from an inconsistency in the input files (case.energysoup or ?) or a code bug is causing I to become larger than the size nmat of BKX(I), BKY(I), or BZX(I), such that it is indexing out of an array. To check if that is what is happening, I would try

Re: [Wien] berryPI

> and >> Max Planck Institute for Chemical Physics of Solids >> 01187 Dresden >> >> Von: wien-boun...@zeus.theochem.tuwien.ac.at [ >> wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Sheikh Jamil >> Ahmed [sahm...@l

Re: [Wien] berryPI code

What is the output of Elias's grep command on your system? For example, in a terminal, you should see something like: username@computername:~/Desktop$ grep Id: $WIENROOT/SRC_w2w/{almgen.F,l2mmn.f,main.f} /home/username/WIEN2k/SRC_w2w/almgen.F:!!! $Id: almgen.F 167 2014-02-03 09:43:33Z assmann

Re: [Wien] berryPI code

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/09/2015 06:22 PM, nilofar hadaeghi wrote: > I really thank You. I will try to find these lines in the source > code of w2w but any further help would be desirable. BerryPI > Version 1.2 Python version: 2.7.3 Numpy version: 1.6.2 At least on

Re: [Wien] berryPI code

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Thanks everybody for chiming in :-). On 09/09/2015 06:36 PM, Víctor Luaña Cabal wrote: > grep -B 5 -A 5 Id: SRC_w2w/{almgen.F,l2mmn.f,main.f} That is very useful in many cases (or just ‘-C 5’, FWIW), but in this case, the one line is really all that

Re: [Wien] berryPI code

>> grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f} Let me explain a little the command by Elias: grep Id: SRC_w2w/{almgen.F,l2mmn.f,main.f} --- - 1 1 1: text to find 2: set of files to explore. Three files in this case. A even improved

Re: [Wien] berryPI code

The output is exactly what has been mentioned in the Gavin Abo's mail as is copied below: /usr/local/codes/wien2k/v14.2/SRC_w2w/almgen.F:!!! $Id: almgen.F 167 2014-02-03 09:43:33Z assmann $ /usr/local/codes/wien2k/v14.2/SRC_w2w/l2mmn.f:!!! $Id: l2mmn.f 167 2014-02-03 09:43:33Z assmann $

Re: [Wien] berryPI

t] im Auftrag von Sheikh Jamil > Ahmed [sahm...@lakeheadu.ca] > Gesendet: Dienstag, 8. September 2015 23:06 > An: A Mailing list for WIEN2k users > Betreff: Re: [Wien] berryPI > > I would like to add that EuTiO3 seems to be a multiferroic compound with > ground state being

Re: [Wien] berryPI

___ > Von: wien-boun...@zeus.theochem.tuwien.ac.at > [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Oleg Rubel > [oru...@lakeheadu.ca] > Gesendet: Dienstag, 8. September 2015 01:03 > An: A Mailing list for WIEN2k users > Betreff: Re: [Wien] berryPI > >

Re: [Wien] berryPI

To address your questions... > I4/mcm is centrosymmetric. I studied the tutorial related to GaN and it > helped me very much. So I conclude to calculate the difference in > polarization, two structures that at least one of them should not be > centrosymmetric are needed, Is it correct? That’s

Re: [Wien] berryPI code

I tried to implement this run this command :x w2w -up -so but I again faced the following error: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLine Source w2wc 0042E242 almgen_ 120

Re: [Wien] berryPI code

I afraid you need to dig into the source code of w2w and see what is going on in these lines. Oleg > On Sep 8, 2015, at 17:57, nilofar hadaeghi wrote: > > I tried to implement this run this command :x w2w -up -so > but I again faced the following error: > > forrtl:

Re: [Wien] berryPI

I would like to add that EuTiO3 seems to be a multiferroic compound with ground state being antiferromagnetic- paraelectric system (I4/mcm). Then, under some compressive or tensile epitaxial strain, several types of transition is possible (For example, antiferromagnetic- ferroelectric or

Re: [Wien] berryPI

tut of Inorganic and Analytical Chemistry >> > Johannes Gutenberg - University >> > 55099 Mainz >> > and >> > Max Planck Institute for Chemical Physics of Solids >> > 01187 Dresden >> > ________ >> > V

[Wien] berryPI

Dear all I have studied some papers whose authors are S.J.Ahmed or O.Rubel in which building the centrosymmetric and noncentrosymmetric structure for the calculation of spontaneous polarization has been explained, but it is still ambiguous for me. Could you please help me whether the

[Wien] berryPI code

Dear all I am working on the berryPI code and I have faced the following error. Can anyine help me please? Best regards, [hadaeghi@cm6 YbB6]$ berrypi -o -j -k10:10:10 [ BerryPI ] +++Version 1.2 (Mar 12, 2014) [ BerryPI ] Python version: 2.7.3 [ BerryPI ] Numpy version: 1.6.2 [ BerryPI ]

Re: [Wien] berryPI code

The error suggests that "x w2w -so -up" did not go through. Please try to run this command manually in the same directory, just to confirm the error. Also there is a trace back information in your segfault report. I would go into specified lines of the sources code and look for hints. I assume

[Wien] BerryPI error

Hello Mostefa, I am glad the code finally worked for your installation. I would suggest to try BiCoO3 first without the spin polarization. The spin polarization is presently not captured in BerryPI. Could you please expand on why do you need SP? I never used DFT+U, so I cannot make a comment

[Wien] BerryPI error

Dear?Oleg Rubel, I have tried the BerryPI code, but I have got this error message: Traceback (most recent call last): ??File ~/Software/BerryPI/berrypi, line 14, in module ?? ?import calculations as b_PyCalc ??File ~/Software/BerryPI/calculations.py, line 20, in module ?? ?from collections

[Wien] BerryPI error

Dear Mostefa, For BerryPI to work python2.6 won't work. You will need python2.7. The reason for this is BerryPI uses some library that are only available in python2.7. For your assistance,Here are the BerryPI dependencies - WIEN2k (tested against 11.1 Release 05/04/2011) - WIEN2WANNIER

[Wien] BerryPI: a new add-on to Wien2k for calculation of polarization properties

Dear Wien2k Community: we would like to announce a new tool for studying polarization-related properties. It enables calculation of the spontaneous polarization and Born effective charges using the Berry phase approach. You can find it now at the Unsupported software goodies section