Re: [Wien] Structure optimization of Beta -Sn

[Peter Blaha]

As far as I know, cif2struct supports only the official names of the 230 
space groups as listed eg. at the Bilbao cryst. server, but not the 
(older ??)  _space_group_name_H-M_altconvention.


For SG # 141 only I41/amd  is supported.

Only for low symmetry SGs with different setting, more than one name is 
supported, eg.

 50, 8,3,'Pban','-P-2zab;-2xb  ', &
 50, 8,3,'Pncb','-P-2xbc;-2yc  ', &
 50, 8,3,'Pcna','-P-2yca;-2za  '/

As far as I know, for parsing the cif files official subroutines from 
IUCR were used, but maybe they have been updated by now or only a subset 
was used or this cif file does not obey the standard.



Am 04.06.2020 um 10:00 schrieb Tran, Fabien:

With your modified cif file, I obtain at the end of init_lapw a struct file 
which has two atoms per cell. Since there is no atoms at the corners, it is 
visually not 100% clear that it is the correct beta-Sn, but I guess it is (?).

I am wondering where the problem with original cif file comes from. From 
cif2struct or a non-conventional format of the cif file? Maybe Peter knows.


From: Wien  on behalf of Xavier Rocquefelte 

Sent: Thursday, June 4, 2020 9:28 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Structure optimization of Beta -Sn

Indeed, I used the one from VESTA! Yesteray night I was working in
parallel ;)

Here is the file I previously sent with modification by hand ... the cif
format was not totally supported by cif2struct.

Regards

Xavier
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--
--
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- 


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Re: [Wien] Adding U value to s orbital

[Peter Blaha]

Try it. I doubt that you will get the desired result.

Am 04.06.2020 um 20:12 schrieb shamik chakrabarti:

Dear Prof. Blaha,

                        I am,trying to reproduce the results of the 
following paper;

https://aip.scitation.org/doi/abs/10.1063/1.4948434

However, the problem is solved by following your advice on a similar 
kind of problem as asked by me in the mailing list. I have copied 
case.dmatup to case.dmatdn and run runsp_lapw.& it is converging now.


with regards,

On Thu, 4 Jun 2020 at 23:14, shamik chakrabarti 
mailto:shamik15041...@gmail.com>> wrote:


Dear Prof. Blaha,

                          I am trying to reproduce the results from
the attached paper.

with regards,

On Thu, 4 Jun 2020 at 22:58, Peter Blaha
mailto:pbl...@theochem.tuwien.ac.at>>
wrote:

It is completely unphysically to do LDA+U for a Sn-s orbital.

Wien2k does not support this.

Am 04.06.2020 um 18:17 schrieb shamik chakrabarti:
 > Dear Wien2k users,
 >
 >                                  I am trying to add a U =
1.75 eV =
 > 0.1287 Ry to the s orbital of Sn atom. I have
modified case.inorb as below;
 >
 >
 > 1  1   0                     nmod, natorb, ipr
 > PRATT  1.0                    BROYD/PRATT, mixing
 >    1  1 0                          iatom nlorb, lorb
 >    1                              nsic 0..AFM, 1..SIC, 2..HFM
 >
 >     0.1287 0.00        U J (Ry)   Note: we recommend to use
U_eff = U-J
 > and J=0
 >
 > *Is the modification is correct?*
 >
 > However, *I am not getting orb -up/dn during SCF cycle*.The
iterations
 > are moving as below;
 >
 >   cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)
 >
 >  >   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io
0pf+0w
 >  >   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58
270.6% 0+0k
 > 0+31760io 0pf+0w
 >  >   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11
266.8% 0+0k
 > 0+29896io 0pf+0w
 >  >   lapw2 -up       -orb (20:52:18) 10.4u 6.1s 0:12.68
130.9% 0+0k
 > 0+1616io 0pf+0w
 >  >   lapw2 -dn       -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5%
0+0k
 > 0+1528io 0pf+0w
 >  >   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k
0+240io 0pf+0w
 >  >   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k
0+240io 0pf+0w
 >  >   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k
0+1408io 0pf+0w
 > :ENERGY convergence:  0 0.0001 0
 > :CHARGE convergence:  0 0. 0
 >
 > Looking forward to listen from you.
 >
 > with regards,
 > --
 > Dr. Shamik Chakrabarti
 > Research Fellow
 > Department of Physics
 > Indian Institute of Technology Patna
 > Bihta-801103
 > Patna
 > Bihar, India
 >
 > ___
 > 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
 >

-- 
--

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.at
    WIEN2k: http://www.wien2k.at
WWW:

http://www.imc.tuwien.ac.at/tc_blaha-


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-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India



--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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--
Peter 

Re: [Wien] Adding U value to s orbital

[shamik chakrabarti]

Dear Prof. Blaha,

   I am,trying to reproduce the results of the
following paper;
https://aip.scitation.org/doi/abs/10.1063/1.4948434

However, the problem is solved by following your advice on a similar kind
of problem as asked by me in the mailing list. I have copied case.dmatup to
case.dmatdn and run runsp_lapw.& it is converging now.

with regards,

On Thu, 4 Jun 2020 at 23:14, shamik chakrabarti 
wrote:

> Dear Prof. Blaha,
>
>  I am trying to reproduce the results from the
> attached paper.
>
> with regards,
>
> On Thu, 4 Jun 2020 at 22:58, Peter Blaha 
> wrote:
>
>> It is completely unphysically to do LDA+U for a Sn-s orbital.
>>
>> Wien2k does not support this.
>>
>> Am 04.06.2020 um 18:17 schrieb shamik chakrabarti:
>> > Dear Wien2k users,
>> >
>> >  I am trying to add a U = 1.75 eV =
>> > 0.1287 Ry to the s orbital of Sn atom. I have modified case.inorb as
>> below;
>> >
>> >
>> > 1  1   0 nmod, natorb, ipr
>> > PRATT  1.0BROYD/PRATT, mixing
>> >1  1 0  iatom nlorb, lorb
>> >1  nsic 0..AFM, 1..SIC, 2..HFM
>> >
>> > 0.1287 0.00U J (Ry)   Note: we recommend to use U_eff = U-J
>> > and J=0
>> >
>> > *Is the modification is correct?*
>> >
>> > However, *I am not getting orb -up/dn during SCF cycle*.The iterations
>> > are moving as below;
>> >
>> >   cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)
>> >
>> >  >   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
>> >  >   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k
>> > 0+31760io 0pf+0w
>> >  >   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k
>> > 0+29896io 0pf+0w
>> >  >   lapw2 -up   -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k
>> > 0+1616io 0pf+0w
>> >  >   lapw2 -dn   -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k
>> > 0+1528io 0pf+0w
>> >  >   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>> >  >   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>> >  >   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io
>> 0pf+0w
>> > :ENERGY convergence:  0 0.0001 0
>> > :CHARGE convergence:  0 0. 0
>> >
>> > Looking forward to listen from you.
>> >
>> > with regards,
>> > --
>> > Dr. Shamik Chakrabarti
>> > Research Fellow
>> > Department of Physics
>> > Indian Institute of Technology Patna
>> > Bihta-801103
>> > Patna
>> > Bihar, India
>> >
>> > ___
>> > 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
>> >
>>
>> --
>> --
>> 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
>>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Adding U value to s orbital

[Peter Blaha]

It is completely unphysically to do LDA+U for a Sn-s orbital.

Wien2k does not support this.

Am 04.06.2020 um 18:17 schrieb shamik chakrabarti:

Dear Wien2k users,

                                 I am trying to add a U = 1.75 eV = 
0.1287 Ry to the s orbital of Sn atom. I have modified case.inorb as below;



1  1   0                     nmod, natorb, ipr
PRATT  1.0                    BROYD/PRATT, mixing
   1  1 0                          iatom nlorb, lorb
   1                              nsic 0..AFM, 1..SIC, 2..HFM

    0.1287 0.00        U J (Ry)   Note: we recommend to use U_eff = U-J 
and J=0


*Is the modification is correct?*

However, *I am not getting orb -up/dn during SCF cycle*.The iterations 
are moving as below;


  cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)

 >   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
 >   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k 
0+31760io 0pf+0w
 >   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k 
0+29896io 0pf+0w
 >   lapw2 -up       -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k 
0+1616io 0pf+0w
 >   lapw2 -dn       -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k 
0+1528io 0pf+0w

 >   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
 >   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
 >   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io 0pf+0w
:ENERGY convergence:  0 0.0001 0
:CHARGE convergence:  0 0. 0

Looking forward to listen from you.

with regards,
--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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--
--
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- 


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Re: [Wien] Adding U value to s orbital

[shamik chakrabarti]

case.dmatdn is empty while case.dmatup is written..

On Thu, 4 Jun 2020 at 22:47, shamik chakrabarti 
wrote:

> Dear  Tran,
>
>  Somehow the orb -up/dn is not working for l=0 (s
> orbital). After running x orb -up I am getting the following error;
> t line 322 of file init.f (unit = 9, file = 'Sn_U_S_V.dmatdn')
> Fortran runtime error: End of file
>
> Error termination. Backtrace:
> #0  0x148fb536396a
> #1  0x148fb53644c5
> #2  0x148fb5364cad
> #3  0x148fb556935b
> #4  0x148fb55621c6
> #5  0x148fb5563a69
> #6  0x56134d3c8641
> #7  0x56134d3c182f
> #8  0x56134d3c12ae
> #9  0x148fb4fd909a
> #10  0x56134d3c12d9
> #11  0x
> 0.0u 0.0s 0:00.01 0.0% 0+0k 0+32io 0pf+0w
> error: command   /usr/local/Wien2k/orb uporb.def   failed
>
> Looking forward to listen from you.
>
> with regards.
>
> On Thu, 4 Jun 2020 at 21:56, Tran, Fabien 
> wrote:
>
>> Slides 29-30:
>>
>> http://www.wien2k.at/events/ws2019/Tran_xc.pdf
>>
>>
>> --
>> *From:* Wien  on behalf of
>> shamik chakrabarti 
>> *Sent:* Thursday, June 4, 2020 6:17 PM
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* [Wien] Adding U value to s orbital
>>
>> Dear Wien2k users,
>>
>> I am trying to add a U = 1.75 eV = 0.1287
>> Ry to the s orbital of Sn atom. I have modified case.inorb as below;
>>
>>
>> 1  1   0 nmod, natorb, ipr
>> PRATT  1.0BROYD/PRATT, mixing
>>   1  1 0  iatom nlorb, lorb
>>   1  nsic 0..AFM, 1..SIC, 2..HFM
>>
>>0.1287 0.00U J (Ry)   Note: we recommend to use U_eff = U-J
>> and J=0
>>
>> *Is the modification is correct?*
>>
>> However, *I am not getting orb -up/dn during SCF cycle*.The iterations
>> are moving as below;
>>
>>  cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)
>>
>> >   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
>> >   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k
>> 0+31760io 0pf+0w
>> >   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k
>> 0+29896io 0pf+0w
>> >   lapw2 -up   -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k
>> 0+1616io 0pf+0w
>> >   lapw2 -dn   -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k
>> 0+1528io 0pf+0w
>> >   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>> >   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>> >   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io 0pf+0w
>> :ENERGY convergence:  0 0.0001 0
>> :CHARGE convergence:  0 0. 0
>>
>> Looking forward to listen from you.
>>
>> with regards,
>> --
>> Dr. Shamik Chakrabarti
>> Research Fellow
>> Department of Physics
>> Indian Institute of Technology Patna
>> Bihta-801103
>> Patna
>> Bihar, India
>> ___
>> 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
>>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Adding U value to s orbital

[shamik chakrabarti]

Dear  Tran,

 Somehow the orb -up/dn is not working for l=0 (s orbital).
After running x orb -up I am getting the following error;
t line 322 of file init.f (unit = 9, file = 'Sn_U_S_V.dmatdn')
Fortran runtime error: End of file

Error termination. Backtrace:
#0  0x148fb536396a
#1  0x148fb53644c5
#2  0x148fb5364cad
#3  0x148fb556935b
#4  0x148fb55621c6
#5  0x148fb5563a69
#6  0x56134d3c8641
#7  0x56134d3c182f
#8  0x56134d3c12ae
#9  0x148fb4fd909a
#10  0x56134d3c12d9
#11  0x
0.0u 0.0s 0:00.01 0.0% 0+0k 0+32io 0pf+0w
error: command   /usr/local/Wien2k/orb uporb.def   failed

Looking forward to listen from you.

with regards.

On Thu, 4 Jun 2020 at 21:56, Tran, Fabien  wrote:

> Slides 29-30:
>
> http://www.wien2k.at/events/ws2019/Tran_xc.pdf
>
>
> --
> *From:* Wien  on behalf of
> shamik chakrabarti 
> *Sent:* Thursday, June 4, 2020 6:17 PM
> *To:* A Mailing list for WIEN2k users
> *Subject:* [Wien] Adding U value to s orbital
>
> Dear Wien2k users,
>
> I am trying to add a U = 1.75 eV = 0.1287
> Ry to the s orbital of Sn atom. I have modified case.inorb as below;
>
>
> 1  1   0 nmod, natorb, ipr
> PRATT  1.0BROYD/PRATT, mixing
>   1  1 0  iatom nlorb, lorb
>   1  nsic 0..AFM, 1..SIC, 2..HFM
>
>0.1287 0.00U J (Ry)   Note: we recommend to use U_eff = U-J and
> J=0
>
> *Is the modification is correct?*
>
> However, *I am not getting orb -up/dn during SCF cycle*.The iterations
> are moving as below;
>
>  cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)
>
> >   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
> >   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k
> 0+31760io 0pf+0w
> >   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k
> 0+29896io 0pf+0w
> >   lapw2 -up   -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k
> 0+1616io 0pf+0w
> >   lapw2 -dn   -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k 0+1528io
> 0pf+0w
> >   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
> >   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
> >   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io 0pf+0w
> :ENERGY convergence:  0 0.0001 0
> :CHARGE convergence:  0 0. 0
>
> Looking forward to listen from you.
>
> with regards,
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
> ___
> Wien mailing list
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> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
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>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Adding U value to s orbital

[Tran, Fabien]

Slides 29-30:

http://www.wien2k.at/events/ws2019/Tran_xc.pdf



From: Wien  on behalf of shamik 
chakrabarti 
Sent: Thursday, June 4, 2020 6:17 PM
To: A Mailing list for WIEN2k users
Subject: [Wien] Adding U value to s orbital

Dear Wien2k users,

I am trying to add a U = 1.75 eV = 0.1287 Ry to 
the s orbital of Sn atom. I have modified case.inorb as below;


1  1   0 nmod, natorb, ipr
PRATT  1.0BROYD/PRATT, mixing
  1  1 0  iatom nlorb, lorb
  1  nsic 0..AFM, 1..SIC, 2..HFM

   0.1287 0.00U J (Ry)   Note: we recommend to use U_eff = U-J and J=0

Is the modification is correct?

However, I am not getting orb -up/dn during SCF cycle.The iterations are moving 
as below;

 cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)

>   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
>   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k 0+31760io 
> 0pf+0w
>   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k 0+29896io 
> 0pf+0w
>   lapw2 -up   -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k 0+1616io 
> 0pf+0w
>   lapw2 -dn   -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k 0+1528io 
> 0pf+0w
>   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io 0pf+0w
:ENERGY convergence:  0 0.0001 0
:CHARGE convergence:  0 0. 0

Looking forward to listen from you.

with regards,
--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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[Wien] Adding U value to s orbital

[shamik chakrabarti]

Dear Wien2k users,

I am trying to add a U = 1.75 eV = 0.1287
Ry to the s orbital of Sn atom. I have modified case.inorb as below;


1  1   0 nmod, natorb, ipr
PRATT  1.0BROYD/PRATT, mixing
  1  1 0  iatom nlorb, lorb
  1  nsic 0..AFM, 1..SIC, 2..HFM

   0.1287 0.00U J (Ry)   Note: we recommend to use U_eff = U-J and
J=0

*Is the modification is correct?*

However, *I am not getting orb -up/dn during SCF cycle*.The iterations are
moving as below;

 cycle 2 (Thu Jun  4 20:51:18 IST 2020) (39/98 to go)

>   lapw0   (20:51:18) 8.5u 0.1s 0:06.65 131.2% 0+0k 0+608io 0pf+0w
>   lapw1  -up   -orb   (20:51:25) 50.8u 23.7s 0:27.58 270.6% 0+0k
0+31760io 0pf+0w
>   lapw1  -dn   -orb   (20:51:53) 46.3u 20.6s 0:25.11 266.8% 0+0k
0+29896io 0pf+0w
>   lapw2 -up   -orb (20:52:18) 10.4u 6.1s 0:12.68 130.9% 0+0k 0+1616io
0pf+0w
>   lapw2 -dn   -orb (20:52:31) 9.7u 5.3s 0:11.26 134.5% 0+0k 0+1528io
0pf+0w
>   lcore -up (20:52:42) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>   lcore -dn (20:52:43) 0.0u 0.0s 0:00.02 50.0% 0+0k 0+240io 0pf+0w
>   mixer  -orb (20:52:43) 0.0u 0.0s 0:00.12 108.3% 0+0k 0+1408io 0pf+0w
:ENERGY convergence:  0 0.0001 0
:CHARGE convergence:  0 0. 0

Looking forward to listen from you.

with regards,
-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Xavier Sir,

Thank you so much for your time & suggestions.

with regards,

On Thu, 4 Jun 2020 at 14:55, Xavier Rocquefelte <
xavier.rocquefe...@univ-rennes1.fr> wrote:

> This last input file leads to a correct structure.
>
> Best regards
>
> Xavier
> Le 04/06/2020 à 11:11, shamik chakrabarti a écrit :
>
> Dear Xavier Sir,
>
>   With the modified cif file & origin choice one, I get
> the structure as attached herewith this mail. Kindly let me know if it is
> the structure you are asking for. I am using wien2k 19.1.
>
> with regards
>
> On Thu, 4 Jun 2020 at 13:30, Tran, Fabien 
> wrote:
>
>> With your modified cif file, I obtain at the end of init_lapw a struct
>> file which has two atoms per cell. Since there is no atoms at the corners,
>> it is visually not 100% clear that it is the correct beta-Sn, but I guess
>> it is (?).
>>
>> I am wondering where the problem with original cif file comes from. From
>> cif2struct or a non-conventional format of the cif file? Maybe Peter knows.
>>
>> 
>> From: Wien  on behalf of Xavier
>> Rocquefelte 
>> Sent: Thursday, June 4, 2020 9:28 AM
>> To: wien@zeus.theochem.tuwien.ac.at
>> Subject: Re: [Wien] Structure optimization of Beta -Sn
>>
>> Indeed, I used the one from VESTA! Yesteray night I was working in
>> parallel ;)
>>
>> Here is the file I previously sent with modification by hand ... the cif
>> format was not totally supported by cif2struct.
>>
>> Regards
>>
>> Xavier
>> ___
>> 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
>>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
> ___
> Wien mailing 
> listw...@zeus.theochem.tuwien.ac.athttp://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
>
> --
> 
> Institut des Sciences Chimiques de Rennes (ISCR)
> Univ Rennes - CNRS - UMR6226, 
> Francehttps://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier
> 
> ICAMM2019 : VASP Workshop and International Materials Modelling Conf
> June 26-July 3 2019, Rennes Franceicamm2019.sciencesconf.org  : Registration 
> opening soon, see you there!
>
> ___
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>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Structure optimization of Beta -Sn

[Xavier Rocquefelte]

This last input file leads to a correct structure.

Best regards

Xavier

Le 04/06/2020 à 11:11, shamik chakrabarti a écrit :

Dear Xavier Sir,

                  With the modified cif file & origin choice one, I 
get the structure as attached herewith this mail. Kindly let me know 
if it is the structure you are asking for. I am using wien2k 19.1.


with regards

On Thu, 4 Jun 2020 at 13:30, Tran, Fabien > wrote:


With your modified cif file, I obtain at the end of init_lapw a
struct file which has two atoms per cell. Since there is no atoms
at the corners, it is visually not 100% clear that it is the
correct beta-Sn, but I guess it is (?).

I am wondering where the problem with original cif file comes
from. From cif2struct or a non-conventional format of the cif
file? Maybe Peter knows.


From: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of
Xavier Rocquefelte mailto:xavier.rocquefe...@univ-rennes1.fr>>
Sent: Thursday, June 4, 2020 9:28 AM
To: wien@zeus.theochem.tuwien.ac.at

Subject: Re: [Wien] Structure optimization of Beta -Sn

Indeed, I used the one from VESTA! Yesteray night I was working in
parallel ;)

Here is the file I previously sent with modification by hand ...
the cif
format was not totally supported by cif2struct.

Regards

Xavier
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--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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--

Institut des Sciences Chimiques de Rennes (ISCR)
Univ Rennes - CNRS - UMR6226, France
https://iscr.univ-rennes1.fr/cti/people/permanent-staff/rocquefelte-xavier

ICAMM2019 : VASP Workshop and International Materials Modelling Conf
June 26-July 3 2019, Rennes France
icamm2019.sciencesconf.org  : Registration opening soon, see you there!

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Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Xavier Sir,

  With the modified cif file & origin choice one, I get the
structure as attached herewith this mail. Kindly let me know if it is the
structure you are asking for. I am using wien2k 19.1.

with regards

On Thu, 4 Jun 2020 at 13:30, Tran, Fabien  wrote:

> With your modified cif file, I obtain at the end of init_lapw a struct
> file which has two atoms per cell. Since there is no atoms at the corners,
> it is visually not 100% clear that it is the correct beta-Sn, but I guess
> it is (?).
>
> I am wondering where the problem with original cif file comes from. From
> cif2struct or a non-conventional format of the cif file? Maybe Peter knows.
>
> 
> From: Wien  on behalf of Xavier
> Rocquefelte 
> Sent: Thursday, June 4, 2020 9:28 AM
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: Re: [Wien] Structure optimization of Beta -Sn
>
> Indeed, I used the one from VESTA! Yesteray night I was working in
> parallel ;)
>
> Here is the file I previously sent with modification by hand ... the cif
> format was not totally supported by cif2struct.
>
> Regards
>
> Xavier
> ___
> 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
>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India


Beta_Sn_final_V.struct
Description: Binary data
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Re: [Wien] Structure optimization of Beta -Sn

[Tran, Fabien]

With your modified cif file, I obtain at the end of init_lapw a struct file 
which has two atoms per cell. Since there is no atoms at the corners, it is 
visually not 100% clear that it is the correct beta-Sn, but I guess it is (?).

I am wondering where the problem with original cif file comes from. From 
cif2struct or a non-conventional format of the cif file? Maybe Peter knows.


From: Wien  on behalf of Xavier 
Rocquefelte 
Sent: Thursday, June 4, 2020 9:28 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Structure optimization of Beta -Sn

Indeed, I used the one from VESTA! Yesteray night I was working in
parallel ;)

Here is the file I previously sent with modification by hand ... the cif
format was not totally supported by cif2struct.

Regards

Xavier
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Re: [Wien] Structure optimization of Beta -Sn

[Xavier Rocquefelte]

I have to remove "s" as you did and rewrite the loop with the symmetry 
operations.


It is a problem with the origin choice!

Regards

Xavier





Le 04/06/2020 à 09:33, Tran, Fabien a écrit :


​Dear Xavier,

Your cif file can be converted to struct, but only if I remove ​"s" as 
suggested by Shamik. I tried with cif2struct from old and new versions 
of cWIEN2k. But, I still get the wrong structure at the end of 
init_lapw (4 equivalent atoms). If I understood correctly, you did not 
have these two problems with your cif file?




*From:* Wien  on behalf of 
Xavier Rocquefelte 

*Sent:* Thursday, June 4, 2020 9:13 AM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* Re: [Wien] Structure optimization of Beta -Sn

Dear Fabien

This is strange... Perhaps a conversion problem. Yes I have used the 
following cif file and cif2struct works for me!


Regards

Xavier



Le 04/06/2020 à 09:10, Tran, Fabien a écrit :


Dear Xavier,

I read your email from yesterday, but I thought that his struct 
filewas correct, because I got the same struct file from this cif file:


http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif

But you are right; if I visualize it, I can see that it is not 
beta-Sn. Besides, I can not convert cif to struct other cif files 
like the one that you sent. With cif2struct, I get "unknown space 
group name: I41/amds" and no struct file is generated.


Did cif2struct​ work for you?




*From:* Wien  on behalf of 
Xavier Rocquefelte 

*Sent:* Wednesday, June 3, 2020 11:54 PM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* Re: [Wien] Structure optimization of Beta -Sn

Dear Fabien,

I explained to Shamik that the structure he was using was not correct.

I also sent cif and struct file.

See below a proper case.struct file.

Shamik could you please send email only to the wienlist to avoid 
multiple answers from the list and many people trying to help you 
without having all the details?



blebleble
B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
MODE OF CALC=RELA unit=bohr
 11.019938 11.019938  6.011975 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
  MULT= 2  ISPLIT=-2
   1: X=0. Y=0.2500 Z=0.3750
Sn1    NPT=  781  R0=.1 RMT= 2.5 Z:  50.
LOCAL ROT MATRIX:    1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  16  NUMBER OF SYMMETRY OPERATIONS
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   1
-1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
   2
 0-1 0 0.2500
 1 0 0 0.7500
 0 0 1 0.2500
   3
 0 1 0 0.2500
-1 0 0 0.2500
 0 0 1 0.7500
   4
-1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
   5
 1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   6
 0 1 0 0.2500
 1 0 0 0.7500
 0 0-1 0.2500
   7
 0-1 0 0.2500
-1 0 0 0.2500
 0 0-1 0.7500
   8
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   9
 1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
  10
 0 1 0 0.7500
-1 0 0 0.2500
 0 0-1 0.7500
  11
 0-1 0 0.7500
 1 0 0 0.7500
 0 0-1 0.2500
  12
 1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
  13
-1 0 0 0.
 0 1 0 0.
 0 0 1 0.
  14
 0-1 0 0.7500
-1 0 0 0.2500
 0 0 1 0.7500
  15
 0 1 0 0.7500
 1 0 0 0.7500
 0 0 1 0.2500
  16





Le 03/06/2020 à 21:38, Tran, Fabien a écrit :


Using a RKmax above 7 should not lead to completely wrong results. 
One important point is how the lattice constants a and c 
were varied. In a meaningful way?




*From:* Wien  on behalf of 
shamik chakrabarti 

*Sent:* Wednesday, June 3, 2020 8:40 PM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Structure optimization of Beta -Sn
Dear Dr. Tran,

                  I have used both plain GGA & nlvdw independently & 
in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw 
& 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the 
problem? I am currently going through the literature you have sent..


with regards,

On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote:


At first sight you struct file seems ok, but this is difficult
to help you without more details. For instance: Which functional
have you used? Are you keeping the c/a ratio fixed? Have you
looked into the literature:

https://aip.scitation.org/doi/abs/10.1063/1.4948434



*From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of
shamik chakrabarti mailto:shamik15041...@gmail.com>>

Re: [Wien] Structure optimization of Beta -Sn

[Tran, Fabien]

​Dear Xavier,

Your cif file can be converted to struct, but only if I remove ​"s" as 
suggested by Shamik. I tried with cif2struct from old and new versions of 
cWIEN2k. But, I still get the wrong structure at the end of init_lapw (4 
equivalent atoms). If I understood correctly, you did not have these two 
problems with your cif file?



From: Wien  on behalf of Xavier 
Rocquefelte 
Sent: Thursday, June 4, 2020 9:13 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Structure optimization of Beta -Sn


Dear Fabien

This is strange... Perhaps a conversion problem. Yes I have used the following 
cif file and cif2struct works for me!

Regards

Xavier



Le 04/06/2020 à 09:10, Tran, Fabien a écrit :

Dear Xavier,

I read your email from yesterday, but I thought that his struct file was 
correct, because I got the same struct file from this cif file:

http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif

But you are right; if I visualize it, I can see that it is not beta-Sn.  
Besides, I can not convert cif to struct other cif files like the one that you 
sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct 
file is generated.

Did cif2struct​ work for you?




From: Wien 

 on behalf of Xavier Rocquefelte 

Sent: Wednesday, June 3, 2020 11:54 PM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Structure optimization of Beta -Sn


Dear Fabien,

I explained to Shamik that the structure he was using was not correct.

I also sent cif and struct file.

See below a proper case.struct file.

Shamik could you please send email only to the wienlist to avoid multiple 
answers from the list and many people trying to help you without having all the 
details?


blebleble
B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
MODE OF CALC=RELA unit=bohr
 11.019938 11.019938  6.011975 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
  MULT= 2  ISPLIT=-2
   1: X=0. Y=0.2500 Z=0.3750
Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  16  NUMBER OF SYMMETRY OPERATIONS
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   1
-1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
   2
 0-1 0 0.2500
 1 0 0 0.7500
 0 0 1 0.2500
   3
 0 1 0 0.2500
-1 0 0 0.2500
 0 0 1 0.7500
   4
-1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
   5
 1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   6
 0 1 0 0.2500
 1 0 0 0.7500
 0 0-1 0.2500
   7
 0-1 0 0.2500
-1 0 0 0.2500
 0 0-1 0.7500
   8
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   9
 1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
  10
 0 1 0 0.7500
-1 0 0 0.2500
 0 0-1 0.7500
  11
 0-1 0 0.7500
 1 0 0 0.7500
 0 0-1 0.2500
  12
 1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
  13
-1 0 0 0.
 0 1 0 0.
 0 0 1 0.
  14
 0-1 0 0.7500
-1 0 0 0.2500
 0 0 1 0.7500
  15
 0 1 0 0.7500
 1 0 0 0.7500
 0 0 1 0.2500
  16





Le 03/06/2020 à 21:38, Tran, Fabien a écrit :

Using a RKmax above 7 should not lead to completely wrong results. One 
important point is how the lattice constants a and c were varied. In a 
meaningful way?



From: Wien 

 on behalf of shamik chakrabarti 

Sent: Wednesday, June 3, 2020 8:40 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Structure optimization of Beta -Sn

Dear Dr. Tran,

  I have used both plain GGA & nlvdw independently & in both 
cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do 
you think moving to larger Rmt*Kmax may solve the problem? I am currently going 
through the literature you have sent..

with regards,

On Wed, 3 Jun 2020 at 23:53, Tran, Fabien 
mailto:fabien.t...@tuwien.ac.at>> wrote:

At first sight you struct file seems ok, but this is difficult to help you 
without more details. For instance: Which functional have you used? Are you 
keeping the c/a ratio fixed? Have you looked into the literature:

https://aip.scitation.org/doi/abs/10.1063/1.4948434



From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of shamik chakrabarti 
mailto:shamik15041...@gmail.com>>
Sent: Wednesday, June 3, 2020 8:06 PM
To: A Mailing list for WIEN2k users
Subject: [Wien] Structure optimization of Beta -Sn

Dear wien2k users,

 I am trying to optimize 

Re: [Wien] Structure optimization of Beta -Sn

[Xavier Rocquefelte]

Indeed, I used the one from VESTA! Yesteray night I was working in 
parallel ;)


Here is the file I previously sent with modification by hand ... the cif 
format was not totally supported by cif2struct.


Regards

Xavier
) 2020 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  
All rights reserved.
data_106072-ICSD
_database_code_ICSD 106072
_audit_creation_date 2004-10-01
_audit_update_record 2017-08-01
_chemical_name_common Tin
_chemical_formula_structural Sn
_chemical_formula_sum Sn1
_chemical_name_structure_type Sn(tI4)
_exptl_crystal_density_diffrn 7.29
_diffrn_ambient_temperature 296.
_citation_title

;
X-ray investigation of thermal expansion and atomic thermal vibrations of tin,
indium, and their alloys
;
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Physica Status Solidi B: Basic Solid State Physics' 1981 107 245 253
PSSBBD
loop_
_citation_author_citation_id
_citation_author_name
primary 'Wolcyrz, M.'
primary 'Kubiak, R.'
primary 'Maciejewski, S.'
_cell_length_a 5.8308(2)
_cell_length_b 5.8308(2)
_cell_length_c 3.1810(2)
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 108.15
_cell_formula_units_Z 4
_symmetry_space_group_name_H-M 'I 41/a m d'
_symmetry_Int_Tables_number 141
loop_

loop_
_symmetry_equiv_pos_as_xyz
   'x, y, z'
   '-x+1/2, -y+1/2, z+1/2'
   '-y, x+1/2, z+1/4'
   'y+1/2, -x, z+3/4'
   '-x+1/2, y, -z+3/4'
   'x, -y+1/2, -z+1/4'
   'y+1/2, x+1/2, -z+1/2'
   '-y, -x, -z'
   '-x, -y+1/2, -z+1/4'
   'x+1/2, y, -z+3/4'
   'y, -x, -z'
   '-y+1/2, x+1/2, -z+1/2'
   'x+1/2, -y+1/2, z+1/2'
   '-x, y, z'
   '-y+1/2, -x, z+3/4'
   'y, x+1/2, z+1/4'
   'x+1/2, y+1/2, z+1/2'
   '-x, -y, z'
   '-y+1/2, x, z+3/4'
   'y, -x+1/2, z+1/4'
   '-x, y+1/2, -z+1/4'
   'x+1/2, -y, -z+3/4'
   'y, x, -z'
   '-y+1/2, -x+1/2, -z+1/2'
   '-x+1/2, -y, -z+3/4'
   'x, y+1/2, -z+1/4'
   'y+1/2, -x+1/2, -z+1/2'
   '-y, x, -z'
   'x, -y, z'
   '-x+1/2, y+1/2, z+1/2'
   '-y, -x+1/2, z+1/4'
   'y+1/2, x, z+3/4'

loop_
_atom_type_symbol
_atom_type_oxidation_number
Sn0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Sn1 Sn0+ 4 a 0 0 0 . 1.
loop_
_atom_site_aniso_label
_atom_site_aniso_type_symbol
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
Sn1 Sn0+ 0.0200(2) 0.0200(2) 0.0241(2) 0. 0. 0.
___
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] Structure optimization of Beta -Sn

[Dr. K. C. Bhamu]

hii Shamik,

open the cif file in VESTA and then export it again as a cif file. This new
cif file should work.
Regards
Bhamu


On Thu, Jun 4, 2020 at 12:43 PM Xavier Rocquefelte <
xavier.rocquefe...@univ-rennes1.fr> wrote:

> Dear Fabien
>
> This is strange... Perhaps a conversion problem. Yes I have used the
> following cif file and cif2struct works for me!
>
> Regards
>
> Xavier
>
>
>
> Le 04/06/2020 à 09:10, Tran, Fabien a écrit :
>
> Dear Xavier,
>
> I read your email from yesterday, but I thought that his struct file was
> correct, because I got the same struct file from this cif file:
>
> http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif
>
> But you are right; if I visualize it, I can see that it is not beta-Sn.
> Besides, I can not convert cif to struct other cif files like the one that
> you sent. With cif2struct, I get "unknown space group name: I41/amds" and
> no struct file is generated.
>
> Did cif2struct work for you?
>
>
>
> --
> *From:* Wien 
>  on behalf of Xavier Rocquefelte
>  
> *Sent:* Wednesday, June 3, 2020 11:54 PM
> *To:* wien@zeus.theochem.tuwien.ac.at
> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>
>
> Dear Fabien,
>
> I explained to Shamik that the structure he was using was not correct.
>
> I also sent cif and struct file.
>
> See below a proper case.struct file.
>
> Shamik could you please send email only to the wienlist to avoid multiple
> answers from the list and many people trying to help you without having all
> the details?
>
>
> blebleble
> B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
> MODE OF CALC=RELA unit=bohr
>  11.019938 11.019938  6.011975 90.00 90.00 90.00
> ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
>   MULT= 2  ISPLIT=-2
>1: X=0. Y=0.2500 Z=0.3750
> Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
> LOCAL ROT MATRIX:1.000 0.000 0.000
>  0.000 1.000 0.000
>  0.000 0.000 1.000
>   16  NUMBER OF SYMMETRY OPERATIONS
>  1 0 0 0.
>  0 1 0 0.
>  0 0 1 0.
>1
> -1 0 0 0.5000
>  0-1 0 0.
>  0 0 1 0.5000
>2
>  0-1 0 0.2500
>  1 0 0 0.7500
>  0 0 1 0.2500
>3
>  0 1 0 0.2500
> -1 0 0 0.2500
>  0 0 1 0.7500
>4
> -1 0 0 0.5000
>  0 1 0 0.
>  0 0-1 0.5000
>5
>  1 0 0 0.
>  0-1 0 0.
>  0 0-1 0.
>6
>  0 1 0 0.2500
>  1 0 0 0.7500
>  0 0-1 0.2500
>7
>  0-1 0 0.2500
> -1 0 0 0.2500
>  0 0-1 0.7500
>8
> -1 0 0 0.
>  0-1 0 0.
>  0 0-1 0.
>9
>  1 0 0 0.5000
>  0 1 0 0.
>  0 0-1 0.5000
>   10
>  0 1 0 0.7500
> -1 0 0 0.2500
>  0 0-1 0.7500
>   11
>  0-1 0 0.7500
>  1 0 0 0.7500
>  0 0-1 0.2500
>   12
>  1 0 0 0.5000
>  0-1 0 0.
>  0 0 1 0.5000
>   13
> -1 0 0 0.
>  0 1 0 0.
>  0 0 1 0.
>   14
>  0-1 0 0.7500
> -1 0 0 0.2500
>  0 0 1 0.7500
>   15
>  0 1 0 0.7500
>  1 0 0 0.7500
>  0 0 1 0.2500
>   16
>
>
>
>
>
> Le 03/06/2020 à 21:38, Tran, Fabien a écrit :
>
> Using a RKmax above 7 should not lead to completely wrong results.
> One important point is how the lattice constants a and c were varied. In a
> meaningful way?
>
>
> --
> *From:* Wien 
>  on behalf of shamik chakrabarti
>  
> *Sent:* Wednesday, June 3, 2020 8:40 PM
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>
> Dear Dr. Tran,
>
>   I have used both plain GGA & nlvdw independently & in
> both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for
> GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am
> currently going through the literature you have sent..
>
> with regards,
>
> On Wed, 3 Jun 2020 at 23:53, Tran, Fabien 
> wrote:
>
>> At first sight you struct file seems ok, but this is difficult to help
>> you without more details. For instance: Which functional have you used? Are
>> you keeping the c/a ratio fixed? Have you looked into the literature:
>>
>> https://aip.scitation.org/doi/abs/10.1063/1.4948434
>>
>>
>> --
>> *From:* Wien  on behalf of
>> shamik chakrabarti 
>> *Sent:* Wednesday, June 3, 2020 8:06 PM
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* [Wien] Structure optimization of Beta -Sn
>>
>> Dear wien2k users,
>>
>>  I am trying to optimize the structure of
>> Beta - Sn. However, even after 20% increment of the volume there is no sign
>> of energy minima. I am attaching the struct file herewith this mail
>> for your consideration.
>>
>> Looking forward to hearing from you.
>>
>> with regards,
>>
>> --
>> Dr. Shamik Chakrabarti
>> Research Fellow
>> Department 

Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Dr. Tran,
  You have to remove the "s" from  "I41/amds" & then
you will get the struct. However, the struct file is always giving 4
equivalent atoms/unit cell.

with regards,

On Thu, 4 Jun 2020 at 12:40, Tran, Fabien  wrote:

> Dear Xavier,
>
> I read your email from yesterday, but I thought that his struct file was
> correct, because I got the same struct file from this cif file:
>
> http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif
>
> But you are right; if I visualize it, I can see that it is not beta-Sn.
> Besides, I can not convert cif to struct other cif files like the one that
> you sent. With cif2struct, I get "unknown space group name: I41/amds" and
> no struct file is generated.
>
> Did cif2struct​ work for you?
>
>
>
> --
> *From:* Wien  on behalf of
> Xavier Rocquefelte 
> *Sent:* Wednesday, June 3, 2020 11:54 PM
> *To:* wien@zeus.theochem.tuwien.ac.at
> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>
>
> Dear Fabien,
>
> I explained to Shamik that the structure he was using was not correct.
>
> I also sent cif and struct file.
>
> See below a proper case.struct file.
>
> Shamik could you please send email only to the wienlist to avoid multiple
> answers from the list and many people trying to help you without having all
> the details?
>
>
> blebleble
> B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
> MODE OF CALC=RELA unit=bohr
>  11.019938 11.019938  6.011975 90.00 90.00 90.00
> ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
>   MULT= 2  ISPLIT=-2
>1: X=0. Y=0.2500 Z=0.3750
> Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
> LOCAL ROT MATRIX:1.000 0.000 0.000
>  0.000 1.000 0.000
>  0.000 0.000 1.000
>   16  NUMBER OF SYMMETRY OPERATIONS
>  1 0 0 0.
>  0 1 0 0.
>  0 0 1 0.
>1
> -1 0 0 0.5000
>  0-1 0 0.
>  0 0 1 0.5000
>2
>  0-1 0 0.2500
>  1 0 0 0.7500
>  0 0 1 0.2500
>3
>  0 1 0 0.2500
> -1 0 0 0.2500
>  0 0 1 0.7500
>4
> -1 0 0 0.5000
>  0 1 0 0.
>  0 0-1 0.5000
>5
>  1 0 0 0.
>  0-1 0 0.
>  0 0-1 0.
>6
>  0 1 0 0.2500
>  1 0 0 0.7500
>  0 0-1 0.2500
>7
>  0-1 0 0.2500
> -1 0 0 0.2500
>  0 0-1 0.7500
>8
> -1 0 0 0.
>  0-1 0 0.
>  0 0-1 0.
>9
>  1 0 0 0.5000
>  0 1 0 0.
>  0 0-1 0.5000
>   10
>  0 1 0 0.7500
> -1 0 0 0.2500
>  0 0-1 0.7500
>   11
>  0-1 0 0.7500
>  1 0 0 0.7500
>  0 0-1 0.2500
>   12
>  1 0 0 0.5000
>  0-1 0 0.
>  0 0 1 0.5000
>   13
> -1 0 0 0.
>  0 1 0 0.
>  0 0 1 0.
>   14
>  0-1 0 0.7500
> -1 0 0 0.2500
>  0 0 1 0.7500
>   15
>  0 1 0 0.7500
>  1 0 0 0.7500
>  0 0 1 0.2500
>   16
>
>
>
>
>
> Le 03/06/2020 à 21:38, Tran, Fabien a écrit :
>
> Using a RKmax above 7 should not lead to completely wrong results.
> One important point is how the lattice constants a and c were varied. In a
> meaningful way?
>
>
> --
> *From:* Wien 
>  on behalf of shamik chakrabarti
>  
> *Sent:* Wednesday, June 3, 2020 8:40 PM
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>
> Dear Dr. Tran,
>
>   I have used both plain GGA & nlvdw independently & in
> both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for
> GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am
> currently going through the literature you have sent..
>
> with regards,
>
> On Wed, 3 Jun 2020 at 23:53, Tran, Fabien 
> wrote:
>
>> At first sight you struct file seems ok, but this is difficult to help
>> you without more details. For instance: Which functional have you used? Are
>> you keeping the c/a ratio fixed? Have you looked into the literature:
>>
>> https://aip.scitation.org/doi/abs/10.1063/1.4948434
>>
>>
>> --
>> *From:* Wien  on behalf of
>> shamik chakrabarti 
>> *Sent:* Wednesday, June 3, 2020 8:06 PM
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* [Wien] Structure optimization of Beta -Sn
>>
>> Dear wien2k users,
>>
>>  I am trying to optimize the structure of
>> Beta - Sn. However, even after 20% increment of the volume there is no sign
>> of energy minima. I am attaching the struct file herewith this mail
>> for your consideration.
>>
>> Looking forward to hearing from you.
>>
>> with regards,
>>
>> --
>> Dr. Shamik Chakrabarti
>> Research Fellow
>> Department of Physics
>> Indian Institute of Technology Patna
>> Bihta-801103
>> Patna
>> Bihar, India
>> ___
>> Wien mailing list
>> 

Re: [Wien] Structure optimization of Beta -Sn

[Xavier Rocquefelte]

Dear Fabien

This is strange... Perhaps a conversion problem. Yes I have used the 
following cif file and cif2struct works for me!


Regards

Xavier



Le 04/06/2020 à 09:10, Tran, Fabien a écrit :


Dear Xavier,

I read your email from yesterday, but I thought that his struct 
filewas correct, because I got the same struct file from this cif file:


http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif

But you are right; if I visualize it, I can see that it is not 
beta-Sn.  Besides, I can not convert cif to struct other cif files 
like the one that you sent. With cif2struct, I get "unknown space 
group name: I41/amds" and no struct file is generated.


Did cif2struct​ work for you?




*From:* Wien  on behalf of 
Xavier Rocquefelte 

*Sent:* Wednesday, June 3, 2020 11:54 PM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* Re: [Wien] Structure optimization of Beta -Sn

Dear Fabien,

I explained to Shamik that the structure he was using was not correct.

I also sent cif and struct file.

See below a proper case.struct file.

Shamik could you please send email only to the wienlist to avoid 
multiple answers from the list and many people trying to help you 
without having all the details?



blebleble
B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
MODE OF CALC=RELA unit=bohr
 11.019938 11.019938  6.011975 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
  MULT= 2  ISPLIT=-2
   1: X=0. Y=0.2500 Z=0.3750
Sn1    NPT=  781  R0=.1 RMT= 2.5 Z:  50.
LOCAL ROT MATRIX:    1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  16  NUMBER OF SYMMETRY OPERATIONS
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   1
-1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
   2
 0-1 0 0.2500
 1 0 0 0.7500
 0 0 1 0.2500
   3
 0 1 0 0.2500
-1 0 0 0.2500
 0 0 1 0.7500
   4
-1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
   5
 1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   6
 0 1 0 0.2500
 1 0 0 0.7500
 0 0-1 0.2500
   7
 0-1 0 0.2500
-1 0 0 0.2500
 0 0-1 0.7500
   8
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   9
 1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
  10
 0 1 0 0.7500
-1 0 0 0.2500
 0 0-1 0.7500
  11
 0-1 0 0.7500
 1 0 0 0.7500
 0 0-1 0.2500
  12
 1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
  13
-1 0 0 0.
 0 1 0 0.
 0 0 1 0.
  14
 0-1 0 0.7500
-1 0 0 0.2500
 0 0 1 0.7500
  15
 0 1 0 0.7500
 1 0 0 0.7500
 0 0 1 0.2500
  16





Le 03/06/2020 à 21:38, Tran, Fabien a écrit :


Using a RKmax above 7 should not lead to completely wrong results. 
One important point is how the lattice constants a and c were varied. 
In a meaningful way?




*From:* Wien  on behalf of 
shamik chakrabarti 

*Sent:* Wednesday, June 3, 2020 8:40 PM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Structure optimization of Beta -Sn
Dear Dr. Tran,

                  I have used both plain GGA & nlvdw independently & 
in both cases the results are same. I have used Rmr*Kmax=9 for nlvdw 
& 7 for GGA. Do you think moving to larger Rmt*Kmax may solve the 
problem? I am currently going through the literature you have sent..


with regards,

On Wed, 3 Jun 2020 at 23:53, Tran, Fabien > wrote:


At first sight you struct file seems ok, but this is difficult to
help you without more details. For instance: Which functional
have you used? Are you keeping the c/a ratio fixed? Have you
looked into the literature:

https://aip.scitation.org/doi/abs/10.1063/1.4948434



*From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of
shamik chakrabarti mailto:shamik15041...@gmail.com>>
*Sent:* Wednesday, June 3, 2020 8:06 PM
*To:* A Mailing list for WIEN2k users
*Subject:* [Wien] Structure optimization of Beta -Sn
Dear wien2k users,

                                 I am trying to optimize the
structure of Beta - Sn. However, even after 20% increment of the
volume there is no sign of energy minima. I am attaching the
struct file herewith this mail for your consideration.

Looking forward to hearing from you.

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at

Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Xacier Sir,

   Thank you for your precious time to solve my problem.
The problem I was having, is that after doing cif2struct I am
always getting the struct file attached herewith. Please advise me the
needful.

with regards,

On Thu, 4 Jun 2020 at 12:28, Xavier Rocquefelte <
xavier.rocquefe...@univ-rennes1.fr> wrote:

> Dear Shamik
>
> I will do as I do with my colleagues who are learning how to use WIEN2k ;)
>
> Use the cif file I previously sent. If you directory is named Beta-Sn,
> rename the cif file Beta-Sn.cif.
>
> Then use cif2struct in this way: cif2struct Beta-Sn.cif. It will
> generate Beta-Sn.struct
>
> Then initialize the calculation and read carefully what WIEN2k is saying.
>
> You will see this message when doing sgroup:
>
>  >   sgroup(08:56:30) 0.000u 0.000s 0:00.00 0.0%0+0k 0+8io 0pf+0w
>Names of point group: -4m2   -4m2   D2d
> warning: !!! Struct file is not consistent with space group found.
> Number and name of space group: 141 (I 41/a m d) [origin choice 2]
> warning: !!! Struct file is not consistent with space group found.
> -> check in  TT.outputsgroup  for proper symmetry, compare
> with your struct file and later with  TT.outputs
> sgroup has also produced a new struct file based on your old one.
> If you see warnings above, consider to use the newly generated
> struct file, which you can view (edit) now.
> -> continue with symmetry (old case.struct) or use/edit
> TT.struct_sgroup ? (c/e)
> e
>
> You see that WIEN2k is not happy with this setting and more specifically
> WIEN2k has only one origin choice for this space group (the second one)
> while the structure I sent you and the one you were using is based on
> the origin choice 1. But WIEN2k helps you and proposes to generate the
> structure file with the origin choice 2.
>
> Thus you must use the new file.
>
> e
> -> Do you want to use the new struct file  ? (y/n)
> y
>   next is nn
>  >   nn(08:57:51)  specify nn-bondlength factor: (usually=2) [and
> optionally dlimit, dstmax (about
>1.d-5, 20)]
> 2
>   DSTMAX:   22.004768372
>   iix,iiy,iiz   5   5   5 55.09969
> 55.0996930.059875000
>   NAMED ATOM: Sn1   Z changed to IATNR+999 to determine equivalency
>
>  ATOM  1  Sn1ATOM  1  Sn1
>   RMT(  1)=2.5 AND RMT(  1)=2.5
>   SUMS TO 5.0  LT.  NN-DIST= 5.71128
> NN ENDS
> 0.004u 0.000s 0:01.51 0.0%0+0k 0+32io 0pf+0w
> -> check in  TT.outputnn  for overlapping spheres,
> coordination and nearest neighbor distances
> -> continue with sgroup or edit the TT.struct file (c/e)
> c
>   next is sgroup
>  >   sgroup(08:58:02) 0.000u 0.000s 0:00.00 0.0%0+0k 0+8io 0pf+0w
>Names of point group: -4m2   -4m2   D2d
> Number and name of space group: 141 (I 41/a m d) [origin choice 2]
> -> check in  TT.outputsgroup  for proper symmetry, compare
> with your struct file and later with  TT.outputs
> sgroup has also produced a new struct file based on your old one.
> If you see warnings above, consider to use the newly generated
> struct file, which you can view (edit) now.
> -> continue with symmetry (old case.struct) or use/edit
> TT.struct_sgroup ? (c/e)
> c
>
> And as you can see you have no more warnings.
>
> Best regards,
>
> Xavier
>
> ___
> 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
>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India


Beta_Sn_struct.struct
Description: Binary data
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Re: [Wien] Structure optimization of Beta -Sn

[Tran, Fabien]

Dear Xavier,

I read your email from yesterday, but I thought that his struct file was 
correct, because I got the same struct file from this cif file:

http://rruff.geo.arizona.edu/AMS/download.php?id=13353.cif=cif

But you are right; if I visualize it, I can see that it is not beta-Sn.  
Besides, I can not convert cif to struct other cif files like the one that you 
sent. With cif2struct, I get "unknown space group name: I41/amds" and no struct 
file is generated.

Did cif2struct​ work for you?




From: Wien  on behalf of Xavier 
Rocquefelte 
Sent: Wednesday, June 3, 2020 11:54 PM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Structure optimization of Beta -Sn


Dear Fabien,

I explained to Shamik that the structure he was using was not correct.

I also sent cif and struct file.

See below a proper case.struct file.

Shamik could you please send email only to the wienlist to avoid multiple 
answers from the list and many people trying to help you without having all the 
details?


blebleble
B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
MODE OF CALC=RELA unit=bohr
 11.019938 11.019938  6.011975 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
  MULT= 2  ISPLIT=-2
   1: X=0. Y=0.2500 Z=0.3750
Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  16  NUMBER OF SYMMETRY OPERATIONS
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   1
-1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
   2
 0-1 0 0.2500
 1 0 0 0.7500
 0 0 1 0.2500
   3
 0 1 0 0.2500
-1 0 0 0.2500
 0 0 1 0.7500
   4
-1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
   5
 1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   6
 0 1 0 0.2500
 1 0 0 0.7500
 0 0-1 0.2500
   7
 0-1 0 0.2500
-1 0 0 0.2500
 0 0-1 0.7500
   8
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   9
 1 0 0 0.5000
 0 1 0 0.
 0 0-1 0.5000
  10
 0 1 0 0.7500
-1 0 0 0.2500
 0 0-1 0.7500
  11
 0-1 0 0.7500
 1 0 0 0.7500
 0 0-1 0.2500
  12
 1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
  13
-1 0 0 0.
 0 1 0 0.
 0 0 1 0.
  14
 0-1 0 0.7500
-1 0 0 0.2500
 0 0 1 0.7500
  15
 0 1 0 0.7500
 1 0 0 0.7500
 0 0 1 0.2500
  16





Le 03/06/2020 à 21:38, Tran, Fabien a écrit :

Using a RKmax above 7 should not lead to completely wrong results. One 
important point is how the lattice constants a and c were varied. In a 
meaningful way?



From: Wien 

 on behalf of shamik chakrabarti 

Sent: Wednesday, June 3, 2020 8:40 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Structure optimization of Beta -Sn

Dear Dr. Tran,

  I have used both plain GGA & nlvdw independently & in both 
cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for GGA. Do 
you think moving to larger Rmt*Kmax may solve the problem? I am currently going 
through the literature you have sent..

with regards,

On Wed, 3 Jun 2020 at 23:53, Tran, Fabien 
mailto:fabien.t...@tuwien.ac.at>> wrote:

At first sight you struct file seems ok, but this is difficult to help you 
without more details. For instance: Which functional have you used? Are you 
keeping the c/a ratio fixed? Have you looked into the literature:

https://aip.scitation.org/doi/abs/10.1063/1.4948434



From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of shamik chakrabarti 
mailto:shamik15041...@gmail.com>>
Sent: Wednesday, June 3, 2020 8:06 PM
To: A Mailing list for WIEN2k users
Subject: [Wien] Structure optimization of Beta -Sn

Dear wien2k users,

 I am trying to optimize the structure of Beta 
- Sn. However, even after 20% increment of the volume there is no sign of 
energy minima. I am attaching the struct file herewith this mail for your 
consideration.

Looking forward to hearing from you.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India



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Re: [Wien] Structure optimization of Beta -Sn

[Xavier Rocquefelte]

Dear Shamik

I will do as I do with my colleagues who are learning how to use WIEN2k ;)

Use the cif file I previously sent. If you directory is named Beta-Sn, 
rename the cif file Beta-Sn.cif.


Then use cif2struct in this way: cif2struct Beta-Sn.cif. It will 
generate Beta-Sn.struct


Then initialize the calculation and read carefully what WIEN2k is saying.

You will see this message when doing sgroup:

>   sgroup    (08:56:30) 0.000u 0.000s 0:00.00 0.0%    0+0k 0+8io 0pf+0w
  Names of point group: -4m2   -4m2   D2d
warning: !!! Struct file is not consistent with space group found.
Number and name of space group: 141 (I 41/a m d) [origin choice 2]
warning: !!! Struct file is not consistent with space group found.
-> check in  TT.outputsgroup  for proper symmetry, compare
   with your struct file and later with  TT.outputs
   sgroup has also produced a new struct file based on your old one.
   If you see warnings above, consider to use the newly generated
   struct file, which you can view (edit) now.
-> continue with symmetry (old case.struct) or use/edit 
TT.struct_sgroup ? (c/e)

e

You see that WIEN2k is not happy with this setting and more specifically 
WIEN2k has only one origin choice for this space group (the second one) 
while the structure I sent you and the one you were using is based on 
the origin choice 1. But WIEN2k helps you and proposes to generate the 
structure file with the origin choice 2.


Thus you must use the new file.

e
-> Do you want to use the new struct file  ? (y/n)
y
 next is nn
>   nn    (08:57:51)  specify nn-bondlength factor: (usually=2) [and 
optionally dlimit, dstmax (about

  1.d-5, 20)]
2
 DSTMAX:   22.004768372
 iix,iiy,iiz   5   5   5 55.09969
   55.09969    30.059875000
 NAMED ATOM: Sn1   Z changed to IATNR+999 to determine equivalency

    ATOM  1  Sn1    ATOM  1  Sn1
 RMT(  1)=2.5 AND RMT(  1)=2.5
 SUMS TO 5.0  LT.  NN-DIST= 5.71128
NN ENDS
0.004u 0.000s 0:01.51 0.0%    0+0k 0+32io 0pf+0w
-> check in  TT.outputnn  for overlapping spheres,
   coordination and nearest neighbor distances
-> continue with sgroup or edit the TT.struct file (c/e)
c
 next is sgroup
>   sgroup    (08:58:02) 0.000u 0.000s 0:00.00 0.0%    0+0k 0+8io 0pf+0w
  Names of point group: -4m2   -4m2   D2d
Number and name of space group: 141 (I 41/a m d) [origin choice 2]
-> check in  TT.outputsgroup  for proper symmetry, compare
   with your struct file and later with  TT.outputs
   sgroup has also produced a new struct file based on your old one.
   If you see warnings above, consider to use the newly generated
   struct file, which you can view (edit) now.
-> continue with symmetry (old case.struct) or use/edit 
TT.struct_sgroup ? (c/e)

c

And as you can see you have no more warnings.

Best regards,

Xavier

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Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Xavier Sir,

  I have a request. Could you please send me the struct
file in case.struct format as an attached file to this mail.

with kind regards,

On Thu, 4 Jun 2020 at 11:43, shamik chakrabarti 
wrote:

> Dear Xavier Sir,
>
>Please excuse me to resolve a confusion. I have not
> sent any mail to anybody's personal mail & has sent the mail only to the
> wien2k mailing list. Dr. Tran answers my query as he was the first one to
> answer my query through a mail sent to the mailing list only.
>
> with regards,
>
> On Thu, 4 Jun 2020 at 11:15, shamik chakrabarti 
> wrote:
>
>> Dear Xavier Sir,
>>
>>   Thank you so much for your suggestions. I will
>> strictly follow it.
>>
>> with kind regards,
>>
>> On Thu, 4 Jun 2020 at 03:39, Xavier Rocquefelte <
>> xavier.rocquefe...@univ-rennes1.fr> wrote:
>>
>>> Here is a cif file. You can see that Sn is on a Wyckoff position 4a,
>>> which means that you have 4 equivalent positions in the space group I 41/a
>>> m d.
>>>
>>> In WIEN2k, it leads to a case.struct file having only 2 equivalent
>>> positions, because only the positions in the primitive cell are shown in
>>> the case.struct file and here the cell is body-centered (I).
>>>
>>>
>>> The fact that you have 4 equivalent position in the case.struct file you
>>> sent to the list is clearly an indication that the structure is not
>>> correct.
>>>
>>> In addition, when starting a calculation you should first check the bond
>>> distances from the litterature, which is about 3.02 angtström for Sn-Sn.
>>> More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn
>>> distance.
>>>
>>>
>>> In the structure you sent to the list the Sn-Sn distances were 2.2
>>> angström!!! It is too small for such an element. It is why the geometry
>>> optimization goes wrong. Thus, the first thing to due before doing
>>> "run_lapw" is to check your data. To do so, you must check carefully:
>>>
>>>
>>> - case.outputnn --> bond distances and coordination
>>>
>>> - case.outputs  --> point group for each inequivalent atoms
>>>
>>> ...
>>>
>>>
>>> Regards
>>>
>>> Xavier
>>>
>>>
>>>
>>>
>>>
>>>
>>> Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit :
>>>
>>> Dear Fabien,
>>>
>>> I explained to Shamik that the structure he was using was not correct.
>>>
>>> I also sent cif and struct file.
>>>
>>> See below a proper case.struct file.
>>>
>>> Shamik could you please send email only to the wienlist to avoid
>>> multiple answers from the list and many people trying to help you without
>>> having all the details?
>>>
>>>
>>> blebleble
>>> B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
>>> MODE OF CALC=RELA unit=bohr
>>>  11.019938 11.019938  6.011975 90.00 90.00 90.00
>>> ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
>>>   MULT= 2  ISPLIT=-2
>>>1: X=0. Y=0.2500 Z=0.3750
>>> Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
>>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>>  0.000 1.000 0.000
>>>  0.000 0.000 1.000
>>>   16  NUMBER OF SYMMETRY OPERATIONS
>>>  1 0 0 0.
>>>  0 1 0 0.
>>>  0 0 1 0.
>>>1
>>> -1 0 0 0.5000
>>>  0-1 0 0.
>>>  0 0 1 0.5000
>>>2
>>>  0-1 0 0.2500
>>>  1 0 0 0.7500
>>>  0 0 1 0.2500
>>>3
>>>  0 1 0 0.2500
>>> -1 0 0 0.2500
>>>  0 0 1 0.7500
>>>4
>>> -1 0 0 0.5000
>>>  0 1 0 0.
>>>  0 0-1 0.5000
>>>5
>>>  1 0 0 0.
>>>  0-1 0 0.
>>>  0 0-1 0.
>>>6
>>>  0 1 0 0.2500
>>>  1 0 0 0.7500
>>>  0 0-1 0.2500
>>>7
>>>  0-1 0 0.2500
>>> -1 0 0 0.2500
>>>  0 0-1 0.7500
>>>8
>>> -1 0 0 0.
>>>  0-1 0 0.
>>>  0 0-1 0.
>>>9
>>>  1 0 0 0.5000
>>>  0 1 0 0.
>>>  0 0-1 0.5000
>>>   10
>>>  0 1 0 0.7500
>>> -1 0 0 0.2500
>>>  0 0-1 0.7500
>>>   11
>>>  0-1 0 0.7500
>>>  1 0 0 0.7500
>>>  0 0-1 0.2500
>>>   12
>>>  1 0 0 0.5000
>>>  0-1 0 0.
>>>  0 0 1 0.5000
>>>   13
>>> -1 0 0 0.
>>>  0 1 0 0.
>>>  0 0 1 0.
>>>   14
>>>  0-1 0 0.7500
>>> -1 0 0 0.2500
>>>  0 0 1 0.7500
>>>   15
>>>  0 1 0 0.7500
>>>  1 0 0 0.7500
>>>  0 0 1 0.2500
>>>   16
>>>
>>>
>>>
>>>
>>>
>>> Le 03/06/2020 à 21:38, Tran, Fabien a écrit :
>>>
>>> Using a RKmax above 7 should not lead to completely wrong results.
>>> One important point is how the lattice constants a and c were varied. In a
>>> meaningful way?
>>>
>>>
>>> --
>>> *From:* Wien 
>>>  on behalf of shamik
>>> chakrabarti  
>>> *Sent:* Wednesday, June 3, 2020 8:40 PM
>>> *To:* A Mailing list for WIEN2k users
>>> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>>>
>>> Dear Dr. Tran,
>>>
>>>   I have 

Re: [Wien] Structure optimization of Beta -Sn

[shamik chakrabarti]

Dear Xavier Sir,

   Please excuse me to resolve a confusion. I have not
sent any mail to anybody's personal mail & has sent the mail only to the
wien2k mailing list. Dr. Tran answers my query as he was the first one to
answer my query through a mail sent to the mailing list only.

with regards,

On Thu, 4 Jun 2020 at 11:15, shamik chakrabarti 
wrote:

> Dear Xavier Sir,
>
>   Thank you so much for your suggestions. I will
> strictly follow it.
>
> with kind regards,
>
> On Thu, 4 Jun 2020 at 03:39, Xavier Rocquefelte <
> xavier.rocquefe...@univ-rennes1.fr> wrote:
>
>> Here is a cif file. You can see that Sn is on a Wyckoff position 4a,
>> which means that you have 4 equivalent positions in the space group I 41/a
>> m d.
>>
>> In WIEN2k, it leads to a case.struct file having only 2 equivalent
>> positions, because only the positions in the primitive cell are shown in
>> the case.struct file and here the cell is body-centered (I).
>>
>>
>> The fact that you have 4 equivalent position in the case.struct file you
>> sent to the list is clearly an indication that the structure is not
>> correct.
>>
>> In addition, when starting a calculation you should first check the bond
>> distances from the litterature, which is about 3.02 angtström for Sn-Sn.
>> More precisely one tin is surrounded by 4 tin atoms with the same Sn-Sn
>> distance.
>>
>>
>> In the structure you sent to the list the Sn-Sn distances were 2.2
>> angström!!! It is too small for such an element. It is why the geometry
>> optimization goes wrong. Thus, the first thing to due before doing
>> "run_lapw" is to check your data. To do so, you must check carefully:
>>
>>
>> - case.outputnn --> bond distances and coordination
>>
>> - case.outputs  --> point group for each inequivalent atoms
>>
>> ...
>>
>>
>> Regards
>>
>> Xavier
>>
>>
>>
>>
>>
>>
>> Le 03/06/2020 à 23:54, Xavier Rocquefelte a écrit :
>>
>> Dear Fabien,
>>
>> I explained to Shamik that the structure he was using was not correct.
>>
>> I also sent cif and struct file.
>>
>> See below a proper case.struct file.
>>
>> Shamik could you please send email only to the wienlist to avoid multiple
>> answers from the list and many people trying to help you without having all
>> the details?
>>
>>
>> blebleble
>> B   LATTICE,NONEQUIV.ATOMS:  1 141 I41/amd
>> MODE OF CALC=RELA unit=bohr
>>  11.019938 11.019938  6.011975 90.00 90.00 90.00
>> ATOM   1: X=0.5000 Y=0.2500 Z=0.1250
>>   MULT= 2  ISPLIT=-2
>>1: X=0. Y=0.2500 Z=0.3750
>> Sn1NPT=  781  R0=.1 RMT= 2.5 Z:  50.
>> LOCAL ROT MATRIX:1.000 0.000 0.000
>>  0.000 1.000 0.000
>>  0.000 0.000 1.000
>>   16  NUMBER OF SYMMETRY OPERATIONS
>>  1 0 0 0.
>>  0 1 0 0.
>>  0 0 1 0.
>>1
>> -1 0 0 0.5000
>>  0-1 0 0.
>>  0 0 1 0.5000
>>2
>>  0-1 0 0.2500
>>  1 0 0 0.7500
>>  0 0 1 0.2500
>>3
>>  0 1 0 0.2500
>> -1 0 0 0.2500
>>  0 0 1 0.7500
>>4
>> -1 0 0 0.5000
>>  0 1 0 0.
>>  0 0-1 0.5000
>>5
>>  1 0 0 0.
>>  0-1 0 0.
>>  0 0-1 0.
>>6
>>  0 1 0 0.2500
>>  1 0 0 0.7500
>>  0 0-1 0.2500
>>7
>>  0-1 0 0.2500
>> -1 0 0 0.2500
>>  0 0-1 0.7500
>>8
>> -1 0 0 0.
>>  0-1 0 0.
>>  0 0-1 0.
>>9
>>  1 0 0 0.5000
>>  0 1 0 0.
>>  0 0-1 0.5000
>>   10
>>  0 1 0 0.7500
>> -1 0 0 0.2500
>>  0 0-1 0.7500
>>   11
>>  0-1 0 0.7500
>>  1 0 0 0.7500
>>  0 0-1 0.2500
>>   12
>>  1 0 0 0.5000
>>  0-1 0 0.
>>  0 0 1 0.5000
>>   13
>> -1 0 0 0.
>>  0 1 0 0.
>>  0 0 1 0.
>>   14
>>  0-1 0 0.7500
>> -1 0 0 0.2500
>>  0 0 1 0.7500
>>   15
>>  0 1 0 0.7500
>>  1 0 0 0.7500
>>  0 0 1 0.2500
>>   16
>>
>>
>>
>>
>>
>> Le 03/06/2020 à 21:38, Tran, Fabien a écrit :
>>
>> Using a RKmax above 7 should not lead to completely wrong results.
>> One important point is how the lattice constants a and c were varied. In a
>> meaningful way?
>>
>>
>> --
>> *From:* Wien 
>>  on behalf of shamik
>> chakrabarti  
>> *Sent:* Wednesday, June 3, 2020 8:40 PM
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* Re: [Wien] Structure optimization of Beta -Sn
>>
>> Dear Dr. Tran,
>>
>>   I have used both plain GGA & nlvdw independently & in
>> both cases the results are same. I have used Rmr*Kmax=9 for nlvdw & 7 for
>> GGA. Do you think moving to larger Rmt*Kmax may solve the problem? I am
>> currently going through the literature you have sent..
>>
>> with regards,
>>
>> On Wed, 3 Jun 2020 at 23:53, Tran, Fabien 
>> wrote:
>>
>>> At first sight you struct file seems ok, but this is difficult to help
>>>