Re: [Wien] regarding permission of Wien2k commands
17.11.2016 11:33, Dr. K. C. Bhamu wrote: While playing with unix commands on my machine, I lost permission of all Wien2k commands. Because of this I am not able to run any Wien2k commands. I am getting the following permissions for all commands: -rwxrwxr-x" . How to get rid off this problem? I cannot understand the problem, I have, for example: ls -Rual lapw1 -rwxrwxr-x 1 lyu lyu 2023274 окт. 13 19:05 lapw1 What is wrong in your case? Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] regarding unit of wave vectror
Dear Users/Prof. Peter Please confirm the unit of wave vectror (horizontel axis in band structure): Is it in k [2*pi/bohr] or in k [pi/m]? I am consedring it a 2*pi/bohr. My purpose it to calculate effective mass. So, considering it in 2*pi/bohr, I am converting into pi/m (m is meter) and then calculating coefficdent of the double differentiation. Kind regards Bhamu ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] x space -c
Dear Sir, I have computed the Electronic and optical properties of AlN monolayer which is matched with the available results and in the next step i want to perform same exercise for InN but in the initialization, space group of the InN monolayer couldn't find and error occurs like Error lat==HEXAGONAL in det_pgrp() diff: InN.outputsgroup: No such file or directory Error lat==HEXAGONAL in det_pgrp() 0.000u 0.012s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/IITJHOME/ambeshst/win2k13mpi/sgroup -wi InN.struct -wo InN.struct_sgroup -set-TOL=0.1 failed cif file of the InN is attached through this mail. Before this, i never face such types of problem. so please tell me where is my mistakes -- Thanks & Regards Rajneesh Chaurasiya Research Scholar IIT Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 InN44.cif Description: CIF chemical test ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] orbital moment-mBJ
Dear Wein users I am using mBJ potential to perform spin-polarised calculations on a perovskite structure. The scf file shows spin magnetic moment. Can I have the info about its orbital moment also using "runsp" command as I have used or I need to give some more command . Please reply Regards -- *Komal* ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] question about tetra's choice of Emax
A thought when reading your description of the cases that might give
troubles:
Of course it could simply be that you have so steep bands that one
does not catch an empty band within 1.5+EF Ry. In this case one has to
increase EMAX in case.in1. And yes, if this really happens, one should
give a :WAR ...(and I don't think this is there yet ..., but I would
need a case where this happens).
It seems in hindsight I of all people should have been able to point you
in the direction of ferromagnetic metals for examples where this might
happen. A broad band (4s) and a narrow one (4d) at E_F are Herring's
(1966) basic ingredients for itinerant magnetism.
You have small exchange in the broad 4s-band and a large one in the
narrow 4d-band. One might (correctly) expect Cu with 11 electrons for
these bands to be a happy paramagnet: the spins of 10 e in the d-band
compensate, and the exchange for the one in the 4s is too small to
redistribute anything from there, 4s is spin balanced. Furthermore it
costs too much energy to increase the 4s population above half full, the
exchange gain in an unbalanced 4d is not sufficient. For Ni with 10
electrons available the cost to increase the 4s population from zero is
smaller. The 4d exchange is large enough to gain energy from an
unbalanced arrangement in an unfilled 4d-band and put 0.6 e into 4s. 4s
remains balanced as in Cu, but exchange puts 5 of the 9.4 4d-electrons
up, 4.4 down, resulting in the observed 0.6 muB. The same argument works
for Co, and to my knowledge for Fe, though its less accurate there, and
it breaks down for Mn. So maybe fcc-Fe and fcc-Ni are other examples - I
didn't try.
Thanks again,
Martin
---
Dr. Martin Pieper
Karl-Franzens University
Institute of Physics
Universitätsplatz 5
A-8010 Graz
Austria
Tel.: +43-(0)316-380-8564
Am 17.11.2016 07:46, schrieb Peter Blaha:
Well, besides the :WAR nings, this is a good example for the problem.
Apparently, at Gamma there is a huge "gap" and you find only 9
eigenvalues (bands) up to 2.1 Ry (while on other k-points there are up
to 12 eigenvalues.
Thus, even the output in scf2 is "wrong", the band-range maximum of
band #10 is not 2.08 but will be "above" 2.1 (1.5+EF).
The TETRA method always integrates bandwise, ie. each band
individually and I need an energy at EVERY k-point to do this
integration. In lapw2 there is a crude fix for "missing eigenvalues"
(it creates an arbitrarily large artificial eigenvalue), but in TETRA
it is not done.
It might be save to calculate the "DOS" (and its integral) to some
higher energy, but it is hard to estimate up to which value it is
still save, since I would have to know the band dispersion. It could
be that (in your case ?) only near Gamma a few k-points miss the 10th
band, but in principle it could also be opposite. Since a reliable
E-limit ("1.5-1.9 ?? in your case") is hard to estimate, I've chosen
the "save" way.
Am 17.11.2016 um 00:55 schrieb pieper:
OK, my mistake: I didn't check the scf for :WARN - which I should have
done, at least after running into the problem.
Just for the record a brief account what happened:
-- Cofcc.struct
fcc-Co
F LATTICE,NONEQUIV.ATOMS: 1
MODE OF CALC=RELA unit=ang
6.637022 6.637022 6.637022 90.00 90.00 90.00
ATOM 1: X=0. Y=0. Z=0.
MULT= 1 ISPLIT= 2
Co NPT= 781 R0=0.5000 RMT=2.3300 Z: 27.0
LOCAL ROT MATRIX:1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
48 NUMBER OF SYMMETRY OPERATIONS
.
.
.
(list of sym ops)
---
Initialization via w2web, quick version, spin polarized marked, 1
k
vectors entered (probably not significant), everything else left open
(defaults). Results without any complaints in
- Cofcc.in1 ---
WFFIL EF=.600081718450 (WFFIL, WFPRI, ENFIL, SUPWF)
7.00 104 (R-MT*K-MAX; MAX L IN WF, V-NMT
0.304 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global
APW/LAPW)
10.30 0.000 CONT 1
1 -4.57 0.001 STOP 1
20.30 0.005 CONT 1
00.30 0.000 CONT 1
K-VECTORS FROM UNIT:4 -9.0 1.535 emin / de (emax=Ef+de)
/
nband
--
scf started in w2web without any changes in the menu. It converges in
11
cycles.
When I ploted the DOS from w2web I ran into the problem of Emax.lt.E_F
Looking into the scf's is a good idea:
- Cofcc.scf1up
ATOMIC SPHERE DEPENDENT PARAMETERS FOR ATOM Co
:e__0001: OVERALL ENERGY PARAMETER IS0.4003
OVERALL BASIS SET ON ATOM IS LAPW
:E1_0001: E( 1)=0.4003
APW+lo
:E1_0001: E( 1)= -3.7752 E(BOTTOM)= -3.806 E(TOP)= -3.744 1
2 175
LOCAL ORBITAL
:E2_0001: E( 2)=0.3944 E(BOTTOM)=0.168 E(TOP)=0.621 0
1 124
APW+lo
:E0_0001: E( 0)=0.4003
Re: [Wien] lapwso_mpi error
So you are using the ifort version with the unformatted file read bug. Based on the Intel page at the link in the previous post below, did you try recompiling lapwso_mpi with -O0 or revert to one of the versions of ifort that Intel mentioned to see if it fixed the problem or not? On 11/14/2016 8:34 AM, Md. Fhokrul Islam wrote: Hi Gavin, Thanks for your suggestion. Yes, I am using 16.0.3.210 version of ifort. Debugging such a big file with 'od' seems to be difficult but I will try with a smaller system and see if I get the same error. Fhokrul *From:* Wien on behalf of Gavin Abo *Sent:* Sunday, November 13, 2016 11:40 PM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] lapwso_mpi error Ok, I agree that it is likely not due to the set up of the scratch directory. What version of ifort was used? If you happened to use 16.0.3.210, maybe it is caused by an ifort bug [ https://software.intel.com/en-us/articles/read-failure-unformatted-file-io-psxe-16-update-3 ]. Perhaps you can use the linux "od" command to try to troubleshot and identify what the data mismatch is between the writing and reading of the 3Mn.vectordn_1 file, similar to what is described on the web pages at: https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/269993 https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/270436 https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/268503 Though, it might be harder to diagnose with the large 3Mn.vectordn_1, which looks to be about 12 GB. So you may want to create a mpi SO calculation that creates a smaller case.vectordn_1 for that. On 11/13/2016 7:30 AM, Md. Fhokrul Islam wrote: Hi Gavin, In my .bashrc scratch is defined as $SCRATCH = ./ so if I use the command echo $SCRATCH, it always returns ./ For large jobs, I use local temporary directory that is associated with each node in our system and is given by $SNIC_TMP. This temporary directory is created on fly, so I set $SCRATCH = $SNIC_TMP in my job submission script. As I said this set up works fine if I do MPI calculations without spin-orbit and I get converged results. But if I submit the job after initializing with spin-orbit, it crashes at lapwso. SO I think problem is probably not due to the set up with scratch directory, it is something to do with MPI version of LAPWSO. Thanks for your comment. Fhokrul ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] x space -c
I cannot reproduce the problem you sent. sgroup runs through without problems. However: Your cif file is from VESTA and I'm not sure if the WIEN2k14.1 cif2struct can work with VESTA files correctly. My new one can do. Your cif file is "inaccurate" and since it is P1, our setup cannot fix it. Inaccurate means that the 1/3 and 2/3 positions are not put in with full precision. Change the struct file manually and put: ATOM -1: X=0.6667 Y=0. Z=0.00878300 ATOM -2: X=0. Y=0.6667 Z=0.00878300 Again sgroup works fine and gives hexagonal SG 187 On 11/17/2016 01:07 PM, Rajneesh Chaurasiya wrote: Dear Sir, I have computed the Electronic and optical properties of AlN monolayer which is matched with the available results and in the next step i want to perform same exercise for InN but in the initialization, space group of the InN monolayer couldn't find and error occurs like Error lat==HEXAGONAL in det_pgrp() diff: InN.outputsgroup: No such file or directory Error lat==HEXAGONAL in det_pgrp() 0.000u 0.012s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/IITJHOME/ambeshst/win2k13mpi/sgroup -wi InN.struct -wo InN.struct_sgroup -set-TOL=0.1 failed cif file of the InN is attached through this mail. Before this, i never face such types of problem. so please tell me where is my mistakes -- Thanks & Regards Rajneesh Chaurasiya Research Scholar IIT Jodhpur, India Mob. No. +91-9584499697 +91-7610950803 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/TC_Blaha -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] regarding permission of Wien2k commands
On Thu, Nov 17, 2016 at 01:03:48PM +0530, Dr. K. C. Bhamu wrote:
> Dear Users,
>
> While playing with unix commands on my machine, I lost permission of all
> Wien2k commands. Because of this I am not able to run any Wien2k commands.
>
> I am getting the following permissions for all commands:
>
> -rwxrwxr-x" .
>
> How to get rid off this problem?
1) Go to the directory where the wien2k codes are installed
2) If you are the owner of the files:
chmod -R ugo+r,a+X *
This gives reading permission to the owner (you) and sticky execution
permissions to anybody. Your "-rwxrwxr-x" refects that this is tour desire,
The -R option works recursibely on the directory you are in.
3) You can modify the owner:group propietary of the files with chown.
Current linux installments tend to create ${USER} and ${GROUP} equivalent,
but this is not the best decission if you have coworkers and students
that could share your codes and scripts.
You will need root permisions (or be a sudoer) to change owner:group
of files.
Good luck,
Víctor
--
. ."When are we ready to learn something? Motivation is the
/ `' \ most important step in education."
/(o)(o)\ -- adapted from Adam Steltzner, 2016 (ElPaís)
/`. \/ .'\
/ '`'` \
| \'`'`/ | "You educate a man, you educate a person. You
| |'`'`| | educate a woman, you educate a family."
\/`'`'`'\/ -- Bárbara Valencia, 2016 (NYTimes)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:!
! phone: +34-985-103491 fax: +34-985-103125 !
++
GroupPage:
git-hub:
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Re: [Wien] orbital moment-mBJ
High Komal, please consult the LAPWDM sections in the user guide. There calculation of the orbital moment is explained. Best regards, Martin Pieper --- Dr. Martin Pieper Karl-Franzens University Institute of Physics Universitätsplatz 5 A-8010 Graz Austria Tel.: +43-(0)316-380-8564 Am 17.11.2016 13:35, schrieb Komal Bapna: Dear Wein users I am using mBJ potential to perform spin-polarised calculations on a perovskite structure. The scf file shows spin magnetic moment. Can I have the info about its orbital moment also using "runsp" command as I have used or I need to give some more command . Please reply Regards -- KOMAL ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] [not solved] regarding permission of Wien2k commands
Thank you Dr. Víctor for suggestion.
But, it could not helped me.
I ran the chmod -R ugo+r,a+X * command in the Wien2k dir and the problem
is still same:
-rwxrwxr-x for all files.
regards
Bhamu
On Thu, Nov 17, 2016 at 10:07 PM, Víctor Luaña Cabal <
vic...@fluor.quimica.uniovi.es> wrote:
> On Thu, Nov 17, 2016 at 01:03:48PM +0530, Dr. K. C. Bhamu wrote:
> > Dear Users,
> >
> > While playing with unix commands on my machine, I lost permission of all
> > Wien2k commands. Because of this I am not able to run any Wien2k
> commands.
> >
> > I am getting the following permissions for all commands:
> >
> > -rwxrwxr-x" .
> >
> > How to get rid off this problem?
>
> 1) Go to the directory where the wien2k codes are installed
>
> 2) If you are the owner of the files:
>
> chmod -R ugo+r,a+X *
>
> This gives reading permission to the owner (you) and sticky execution
> permissions to anybody. Your "-rwxrwxr-x" refects that this is tour desire,
> The -R option works recursibely on the directory you are in.
>
> 3) You can modify the owner:group propietary of the files with chown.
>Current linux installments tend to create ${USER} and ${GROUP}
> equivalent,
>but this is not the best decission if you have coworkers and students
>that could share your codes and scripts.
>You will need root permisions (or be a sudoer) to change owner:group
>of files.
>
> Good luck,
> Víctor
>
> --
> . ."When are we ready to learn something? Motivation is the
> / `' \ most important step in education."
>/(o)(o)\ -- adapted from Adam Steltzner, 2016 (ElPaís)
> /`. \/ .'\
> / '`'` \
> | \'`'`/ | "You educate a man, you educate a person. You
> | |'`'`| | educate a woman, you educate a family."
> \/`'`'`'\/ -- Bárbara Valencia, 2016 (NYTimes)
> ===(((==)))==+=
> ! Dr.Víctor Luaña, in silico chemist & prof. !
> ! Departamento de Química Física y Analítica !
> ! Universidad de Oviedo, 33006-Oviedo, Spain !
> ! e-mail:!
> ! phone: +34-985-103491 fax: +34-985-103125 !
> ++
> GroupPage:
> git-hub:
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at: http://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/index.html
>
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Re: [Wien] [not solved] regarding permission of Wien2k commands
On Thu, Nov 17, 2016 at 11:05:21PM +0530, Dr. K. C. Bhamu wrote: > Thank you Dr. Víctor for suggestion. > But, it could not helped me. > I ran the chmod -R ugo+r,a+X * command in the Wien2k dir and the problem > is still same: > > -rwxrwxr-x for all files. Do you mean that every file has those permissions? Including executabables, inputs and uoutputs? In that case you have to use the chmod ro remove permissions or set exactly then to the ones you decide. The permissions at the time of creation of a new file are decided by the umask setting. For instance, if you are using bash your ~/.bashrc shoud containg something like umask 027 that will give you (the owner) rw permission and the x will be provided after compilling and loading, or you can assing it with a chmod un the case you are creating a text script (bash, pytho, awk, ...) and decide to convert the script into a executable. The umask gives also everybody in your group r permissions, and others no permission whatever. Try reading a good user guide on the shell you prefer. It pays the time you dedicate at the beginning. Best regards, V. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] [not solved] regarding permission of Wien2k commands
Yes, this " -rwxrwxr-x" is for all executables in Wien2k. Bhamu On Thu, Nov 17, 2016 at 10:05 AM, Víctor Luaña Cabal < vic...@fluor.quimica.uniovi.es> wrote: > On Thu, Nov 17, 2016 at 11:05:21PM +0530, Dr. K. C. Bhamu wrote: > > Thank you Dr. Víctor for suggestion. > > But, it could not helped me. > > I ran the chmod -R ugo+r,a+X * command in the Wien2k dir and the > problem > > is still same: > > > > -rwxrwxr-x for all files. > > Do you mean that every file has those permissions? Including executabables, > inputs and uoutputs? > > In that case you have to use the chmod ro remove permissions or set > exactly then to the ones you decide. > > The permissions at the time of creation of a new file are decided by > the umask setting. For instance, if you are using bash your ~/.bashrc > shoud containg something like > > umask 027 > > that will give you (the owner) rw permission and the x will be provided > after compilling and loading, or you can assing it with a chmod un the > case you are creating a text script (bash, pytho, awk, ...) and decide > to convert the script into a executable. > > The umask gives also everybody in your group r permissions, and others > no permission whatever. > > Try reading a good user guide on the shell you prefer. It pays the time > you dedicate at the beginning. > > Best regards, > V. > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: http://www.mail-archive.com/ > wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
