Re: [Wien] Optimization of an spinel structure
Trying to answer your comments; SG227 is FCC, that is, the conventional cell has 4 primitive cells the first wyckoff positions are; 8a 1/8,1/8,1/8 8b 3/8,3/8,3/8 16c 0,0,0 16d 1/2,1/2,1/2 32e x,x,x 8a and 8b have 2 atoms in the primitive cell 16c and 16d have 4 32e has 8 MnFe2O4 is a spinel Mn; 8a Fe; 16d O; 32e x=0.2639 The primitive cell has 2 formula units while the conventional cel has 8 formula units then the atomic positions in MnFe2O4.struct are; F LATTICE,NONEQUIV.ATOMS: 3 227_Fd-3m 16.059466 16.059466 16.059466 90.00 90.00 90.00 ATOM 1: X=0.1250 Y=0.1250 Z=0.1250 ATOM 1:X= 0.8750 Y=0.8750 Z=0.8750 Mn NPT= 781 R0=0.5000 RMT=1.8600 Z: 25.000 ATOM -2: X=0.5000 Y=0.5000 Z=0.5000 ATOM -2:X= 0.5000 Y=0.7500 Z=0.7500 ATOM -2:X= 0.7500 Y=0.7500 Z=0.5000 ATOM -2:X= 0.7500 Y=0.5000 Z=0.7500 Fe NPT= 781 R0=0.5000 RMT=2.1500 Z: 26.000 ATOM -3: X=0.2639 Y=0.2639 Z=0.2639 ATOM -3:X= 0.7361 Y=0.7361 Z=0.7361 ATOM -3:X= 0.7361 Y=0.5139 Z=0.5139 ATOM -3:X= 0.2639 Y=0.9861 Z=0.9861 ATOM -3:X= 0.9861 Y=0.9861 Z=0.2639 ATOM -3:X= 0.5139 Y=0.5139 Z=0.7361 ATOM -3:X= 0.5139 Y=0.7361 Z=0.5139 ATOM -3:X= 0.9861 Y=0.2639 Z=0.9861 O NPT= 781 R0=0.0001 RMT=1.6000 Z: 8.000 Now, if one wants to make it antiferro then one posibility is to take two Fe 'up' and two 'dn', and the system becomes; B LATTICE,NONEQUIV.ATOMS: 5 74_Imma 11.355757 11.355757 16.059466 90.00 90.00 90.00 ATOM 1: X=0. Y=0.2500 Z=0.1250 ATOM 1:X= 0. Y=0.7500 Z=0.8750 Mn NPT= 781 R0=0.5000 RMT=1.8600 Z: 25.000 ATOM 2: X=0.2500 Y=0.7500 Z=0.2500 ATOM 2:X= 0.2500 Y=0.2500 Z=0.7500 Fe1NPT= 781 R0=0.5000 RMT=2.1500 Z: 26.000 ATOM 3: X=0. Y=0.5278 Z=0.2639 ATOM 3:X= 0. Y=0.4722 Z=0.7361 ATOM 3:X= 0. Y=0.0278 Z=0.7361 ATOM 3:X= 0. Y=0.9722 Z=0.2639 O 1NPT= 781 R0=0.0001 RMT=1.6000 Z: 8.000 ATOM 4: X=0.7778 Y=0.7500 Z=0.4861 ATOM 4:X= 0. Y=0.2500 Z=0.5139 ATOM 4:X= 0.7778 Y=0.2500 Z=0.5139 ATOM 4:X= 0. Y=0.7500 Z=0.4861 O 2NPT= 781 R0=0.0001 RMT=1.6000 Z: 8.000 ATOM 5: X=0. Y=0. Z=0.5000 ATOM 5:X= 0. Y=0.5000 Z=0.5000 Fe2NPT= 781 R0=0.5000 RMT=2.1500 Z: 26.000 As it can be seen the 8 O atoms in 32e position are now in two groups of 4 O atoms and as I mentioned before the 'runsp -min' will move them in a way that it would break the cubic FCC crystal symmetry. The problem is that Fe in this system has the kagome arangement and antiferro ordering is just a simplification, but the system should be cubic with the SG 227. Saludos Pablo De: Wien en nombre de Fecher, Gerhard Enviado: martes, 2 de noviembre de 2021 05:07 a. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Optimization of an spinel structure Sorry, it depends on the setting for space group 227 whether X=1/4 results in a 8- or 32-fold degenerate position, I did not check which one Wien2k uses (unfortunately one can not use crystallographic Wykoff positions directly). if you have already the 32-fold degenerate site (I guess wien2k reports a smaller cell with 8 sites) then min should find the correct positions by minimizing the forces. The remarks on the magnetic order are not touched by that. Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Physics Johannes Gutenberg - University 55099 Mainz Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von delamora [delam...@unam.mx] Gesendet: Dienstag, 2. November 2021 04:49 An: wien@zeus.theochem.tuwien.ac.at Betreff: [Wien] Optimization of an spinel structure Dear WIEN community, I am trying to optimize a spinel structure. The normal spinel AB2X4 is FCC with SG 227 A: 1/8,1/8,1/8 B: 1/2,1/2,1/2 X: x,x,x x~1/4 so it has 2 free parameters; 'volume' and 'x,x,x' but in my cases B is magnetic and it has antiferromagnetic coupling, B also forms the 3D Kagome structure so it is geometrically frustrated. The volume optimization can be easily done with option 'optimize' but for the 'x' parameter there is a problem; To treat the magnetism the best option, in my opinion, is to put half of the B atoms 'up' and the other half 'dn', there are 4 in the primitive cell, so 2 are 'up' and 2 'dn'. With this, then the FCC cell be
[Wien] 「Password」答复: Mixer error: NEC01 charge leakage_too_largeage too large
[CN] 为了解压加密附件，发送密码通知邮件。 [JP] 暗号化を解除する為のパスワードをお知らせします。 [EN] This message contains the password that can unzip an encrypted attachment. [Message] Date: Wed, 03 Nov 2021 08:24:15 Subject: 答复: [Wien] Mixer error: NEC01 charge leakage_too_large Attached file: TTRSSH_20211103082415.zi_ [Password] GJWdzQ6n ※[CN] 请先更改扩展名“zi_”⇒“zip”，再解压。 ※[JP] 拡張子を"zi_" ⇒"zip"へ変更の上、解凍下さい。 ※[EN] Please change the extension from "zi_" ⇒ to "zip" and then unzip it. ___ 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] Mixer error: NEC01 charge leakage too large
You probably need to send your case.struct & case.in1. Please look at the
instructions for what is needed.
Also, what version?
---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi
On Tue, Nov 2, 2021, 6:43 PM ChenJie wrote:
> Hi,
>
>
>
> I am new to Wien2k. I am trying to run the TiC example and MoS2 example
> from the user guide using Wien2k_21.1, and I was able to go through all the
> steps in init_lapw without any issue, but when I tried to run the scf (via
> run_lapw –p –ec 0.0001), I encountered the issue at the mixer step (after
> lcore), and I have copy-pasted the STDOUT error message below (for mos2):
>
>
>
>
>
> *kpoint*
>
> *mos2.broyd* files present ! You did not save_lapw a previous clculation.*
>
> *You have 60 seconds to kill this job ( ^C or kill 56323 )*
>
> *or the script will rm *.broyd* and continue (use -NI to avoid automatic
> rm)*
>
> * LAPW0 END*
>
> *[1]Done srun -N1 -n4
> /public1/home/sca2456/soft/lapw0_mpi lapw0.def >> .time00*
>
> * LAPW1 END*
>
> *[1] + Done ( ( $remote $machine[$p] "cd
> $PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def ;fixerror_lapw
> ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .*
>
> *stdout1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw
> .stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; grep
> -v \% .temp1_$loop | perl -e "print stderr " )*
>
> *LAPW2 - FERMI; weights written*
>
> * LAPW2 END*
>
> *[1]Done ( ( $remote $machine[$p] "cd
> $PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_${loop}.def
> $loop;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p]*
>
> * ) >& .stdout2_$loop; if ( -f .stdout2_$loop ) bashtime2csh.pl_lapw
> .stdout2_$loop > .temp2_$loop; grep \% .temp2_$loop >> .time2_$loop; grep
> -v \% .temp2_$loop | perl -e "print stderr
> *IN>" )*
>
> * SUMPARA END*
>
> * CORE END*
>
> *ERROR: NEC01 charge leakage too large*
>
>
>
> *> stop error*
>
>
>
>
>
> I read from the manual that this issue could be caused by improper setting
> of RMT, or the energy to separate core from valence states (which defaults
> to -6 Ry), so I played with these two values as well the kpoint mesh size
> during the init_lapw step, but I kept on getting the above error message,
> for both TiC and mos2 system.
>
>
>
> I am wondering what could be causing this error, for example, could it be
> due to some other settings?
>
>
>
> Thank you very much, and please let me know if any more information is
> needed.
>
>
>
> Regards,
>
> Jie
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
>
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> SEARCH the MAILING-LIST at:
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>
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[Wien] Mixer error: NEC01 charge leakage too large
Hi,
I am new to Wien2k. I am trying to run the TiC example and MoS2 example from
the user guide using Wien2k_21.1, and I was able to go through all the steps in
init_lapw without any issue, but when I tried to run the scf (via run_lapw –p
–ec 0.0001), I encountered the issue at the mixer step (after lcore), and I
have copy-pasted the STDOUT error message below (for mos2):
kpoint
mos2.broyd* files present ! You did not save_lapw a previous clculation.
You have 60 seconds to kill this job ( ^C or kill 56323 )
or the script will rm *.broyd* and continue (use -NI to avoid automatic rm)
LAPW0 END
[1]Done srun -N1 -n4
/public1/home/sca2456/soft/lapw0_mpi lapw0.def >> .time00
LAPW1 END
[1] + Done ( ( $remote $machine[$p] "cd
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def ;fixerror_lapw
${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .
stdout1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw .stdout1_$loop >
.temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; grep -v \% .temp1_$loop |
perl -e "print stderr " )
LAPW2 - FERMI; weights written
LAPW2 END
[1]Done ( ( $remote $machine[$p] "cd
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_${loop}.def
$loop;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p]
) >& .stdout2_$loop; if ( -f .stdout2_$loop ) bashtime2csh.pl_lapw
.stdout2_$loop > .temp2_$loop; grep \% .temp2_$loop >> .time2_$loop; grep -v \%
.temp2_$loop | perl -e "print stderr " )
SUMPARA END
CORE END
ERROR: NEC01 charge leakage too large
> stop error
I read from the manual that this issue could be caused by improper setting of
RMT, or the energy to separate core from valence states (which defaults to -6
Ry), so I played with these two values as well the kpoint mesh size during the
init_lapw step, but I kept on getting the above error message, for both TiC and
mos2 system.
I am wondering what could be causing this error, for example, could it be due
to some other settings?
Thank you very much, and please let me know if any more information is needed.
Regards,
Jie
___
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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] Optimization of an spinel structure
Sorry, it depends on the setting for space group 227 whether X=1/4 results in a 8- or 32-fold degenerate position, I did not check which one Wien2k uses (unfortunately one can not use crystallographic Wykoff positions directly). if you have already the 32-fold degenerate site (I guess wien2k reports a smaller cell with 8 sites) then min should find the correct positions by minimizing the forces. The remarks on the magnetic order are not touched by that. Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Physics Johannes Gutenberg - University 55099 Mainz Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von delamora [delam...@unam.mx] Gesendet: Dienstag, 2. November 2021 04:49 An: wien@zeus.theochem.tuwien.ac.at Betreff: [Wien] Optimization of an spinel structure Dear WIEN community, I am trying to optimize a spinel structure. The normal spinel AB2X4 is FCC with SG 227 A: 1/8,1/8,1/8 B: 1/2,1/2,1/2 X: x,x,x x~1/4 so it has 2 free parameters; 'volume' and 'x,x,x' but in my cases B is magnetic and it has antiferromagnetic coupling, B also forms the 3D Kagome structure so it is geometrically frustrated. The volume optimization can be easily done with option 'optimize' but for the 'x' parameter there is a problem; To treat the magnetism the best option, in my opinion, is to put half of the B atoms 'up' and the other half 'dn', there are 4 in the primitive cell, so 2 are 'up' and 2 'dn'. With this, then the FCC cell becomes BCC (SG 74 Imma) and the 8 'X' atoms that were in one wyckoff position are now in two wyckoff positions with 4 atoms in each. So, if the forces are minimized, 'runsp -min', will move these two 'X' groups in directions that will break the original cubic symmetry. One posibility is to make 4 'struct' files, in the original SG 227, with slightly different 'x' positions, for example, the initial x,x,x is; x= 0.254, so I make 4 struct files with; 0.251, 0.253, 0.255, 0.257 after this one should make them antiferromagnetic (SG 74 Imma) then run them separatelly, then one can obtain the optimum 'x' parameter. I tried to use a modified 'optimize.job' but it did not work. I also tried to run these 4 'struct' files in the same directory but I found that when I put the next case.struct into the directory, I had to initiate the system in order to be able to run them. In other words, if I run the system with 1-struct, then for the next 2-struct I cannot just change 1-struct for 2-struct and run. For the case of changes of volume then the optimize.job works fine, but for small changes in 'x' it does not work. I anybody has an idea that would make this case simpler I would apreciate. Thank you anyway Pablo ___ 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] Optimization of an spinel structure
In this particular case, if your x parameter is other then 1/4 then you are not longer in space group 227 already in the non magnetic case, your Wyckoff positions in SG 227 are 16-fold for A and 8 -fold for both B and X degenerate now if you put x = 1/4 + delta, then the site for the X atoms wouldl be 32-fold degenerate (in SG 227) It seems your structure is ill defined from the beginning, you need to use the correct spave group. It seems you just try to use the highest symmetry for a non-magnetic case to model the antiferromagnetic state, this is doubtful. you need to test also other arrangements, check the possible magnetic space groups. Just to mention, if you have a frustrated system with non-collinear spins, then you may not just set them up and down you can do it, but what do you learn ? Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Physics Johannes Gutenberg - University 55099 Mainz Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von delamora [delam...@unam.mx] Gesendet: Dienstag, 2. November 2021 04:49 An: wien@zeus.theochem.tuwien.ac.at Betreff: [Wien] Optimization of an spinel structure Dear WIEN community, I am trying to optimize a spinel structure. The normal spinel AB2X4 is FCC with SG 227 A: 1/8,1/8,1/8 B: 1/2,1/2,1/2 X: x,x,x x~1/4 so it has 2 free parameters; 'volume' and 'x,x,x' but in my cases B is magnetic and it has antiferromagnetic coupling, B also forms the 3D Kagome structure so it is geometrically frustrated. The volume optimization can be easily done with option 'optimize' but for the 'x' parameter there is a problem; To treat the magnetism the best option, in my opinion, is to put half of the B atoms 'up' and the other half 'dn', there are 4 in the primitive cell, so 2 are 'up' and 2 'dn'. With this, then the FCC cell becomes BCC (SG 74 Imma) and the 8 'X' atoms that were in one wyckoff position are now in two wyckoff positions with 4 atoms in each. So, if the forces are minimized, 'runsp -min', will move these two 'X' groups in directions that will break the original cubic symmetry. One posibility is to make 4 'struct' files, in the original SG 227, with slightly different 'x' positions, for example, the initial x,x,x is; x= 0.254, so I make 4 struct files with; 0.251, 0.253, 0.255, 0.257 after this one should make them antiferromagnetic (SG 74 Imma) then run them separatelly, then one can obtain the optimum 'x' parameter. I tried to use a modified 'optimize.job' but it did not work. I also tried to run these 4 'struct' files in the same directory but I found that when I put the next case.struct into the directory, I had to initiate the system in order to be able to run them. In other words, if I run the system with 1-struct, then for the next 2-struct I cannot just change 1-struct for 2-struct and run. For the case of changes of volume then the optimize.job works fine, but for small changes in 'x' it does not work. I anybody has an idea that would make this case simpler I would apreciate. Thank you anyway Pablo ___ 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
