[Wien] Error during abc & gamma (4D) optimization of a monoclinic system
shamik chakrabarti
shamik15041981 at gmail.com
Tue Aug 25 09:05:12 CEST 2020
Dear Prof. Gavin,
Thanks a lot for your help. It is working now.
However, I have another query. After x optimize with the struct file a
message comes as: SPACE GROUP CONTAINS INVERSION
* alpha(3) .gt. 91.0; reset to 90.1. *However, the struct file remains the
same after this message. Hence, should we ignore the message?
with regards,
On Tue, 25 Aug 2020 at 11:57, Gavin Abo <gsabo at crimson.ua.edu> wrote:
> I took your attached Nb2Se3_all_min_initial.struct at [1], kept the
> structure the same but swapped the lattice angles (beta<->gamma), lattice
> constants (b<->c), and atomic positions (y<->z) in StructGen of w2web and
> generated the new symmetry operations for it with "x symmetry" which gave
> the attached Nb2Se3_all_min.struct following the advice at:
>
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html
> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$>
>
> I then ran the 4D "x optimize" on it using WIEN2k 19.2 as given below.
> I'm not able to reproduce what you have described as instead it looks like
> the "x optimize" script changes the gamma angle just fine from the original
> 104.153240 degrees to other angles such as 102.070175 and 106.236305 in
> some of the .struct files.
>
> username at computername:~/wiendata/Nb2Se3_all_min$ ls
> Nb2Se3_all_min.struct
> username at computername:~/wiendata/Nb2Se3_all_min$ x optimize
> ********************************************
> GENERATES STRUCT-FILES AND optimize.job
> PLEASE CHOOSE ONE OF THE FOLLOWING FEATURES:
>
> [1] VARY VOLUME with CONSTANT RATIO A:B:C
> [2] VARY C/A RATIO with CONSTANT VOLUME (tetr and hex lattices)
> [3] VARY C/A RATIO with CONSTANT VOLUME and B/A (orthorh lattice)
> [4] VARY B/A RATIO with CONSTANT VOLUME and C/A (orthorh lattice)
> [5] VARY A and C (2D-case) (tetragonal or hexagonal lattice)
> [6] VARY A, B and C (3D-case) (orthorhombic lattice)
> [7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice)
> [8] VARY C/A RATIO and VOLUME (2D-case) (tetr and hex lattices)
>
> ********************************************
>
> 7
>
> ***************************************************
> Generating
> Nb2Se3_all_min_initial.struct
>
> next time this file will be used as template unless you remove it
> explicitly.
> ***************************************************
> number of structures: 15, 81 (3x3x3x3), 256 (4x4x4x4)
> 15
> PLEASE enter a percentage change of a
> 2
> Nb2Se3_all_min_mon____1.00.struct
>
> 12.153492 17.398148 6.478929104.153240
> Nb2Se3_all_min_mon____2.00.struct
>
> 12.401522 17.398148 6.478929104.153240
> Nb2Se3_all_min_mon____3.00.struct
>
> 12.649552 17.398148 6.478929104.153240
> Nb2Se3_all_min_mon____4.00.struct
>
> 12.401522 17.050185 6.478929104.153240
> Nb2Se3_all_min_mon____5.00.struct
>
> 12.401522 17.746111 6.478929104.153240
> Nb2Se3_all_min_mon____6.00.struct
>
> 12.401522 17.398148 6.349350104.153240
> Nb2Se3_all_min_mon____7.00.struct
>
> 12.401522 17.398148 6.608508104.153240
> Nb2Se3_all_min_mon____8.00.struct
>
> 12.153492 17.050185 6.478929104.153240
> Nb2Se3_all_min_mon____9.00.struct
>
> 12.153492 17.398148 6.349350104.153240
> Nb2Se3_all_min_mon___10.00.struct
>
> 12.401522 17.050185 6.349350104.153240
> Nb2Se3_all_min_mon___11.00.struct
>
> 12.401522 17.398148 6.478929102.070175
> Nb2Se3_all_min_mon___12.00.struct
>
> 12.401522 17.398148 6.478929106.236305
> Nb2Se3_all_min_mon___13.00.struct
>
> 12.153492 17.398148 6.478929102.070175
> Nb2Se3_all_min_mon___14.00.struct
>
> 12.401522 17.050185 6.478929102.070175
> Nb2Se3_all_min_mon___15.00.struct
>
> 12.401522 17.398148 6.349350102.070175
> Now run optimize.job
> 0.0u 0.0s 0:09.80 0.0% 0+0k 0+264io 0pf+0w
>
> username at computername:~/wiendata/Nb2Se3_all_min$ awk 'FNR==4 {print
> FILENAME, substr($5, length($5)-9, length($5))}' *.struct
> Nb2Se3_all_min_initial.struct 104.153240
> Nb2Se3_all_min_mon___10.00.struct 104.153240
> Nb2Se3_all_min_mon____1.00.struct 104.153240
> Nb2Se3_all_min_mon___11.00.struct 102.070175
> Nb2Se3_all_min_mon___12.00.struct 106.236305
> Nb2Se3_all_min_mon___13.00.struct 102.070175
> Nb2Se3_all_min_mon___14.00.struct 102.070175
> Nb2Se3_all_min_mon___15.00.struct 102.070175
> Nb2Se3_all_min_mon____2.00.struct 104.153240
> Nb2Se3_all_min_mon____3.00.struct 104.153240
> Nb2Se3_all_min_mon____4.00.struct 104.153240
> Nb2Se3_all_min_mon____5.00.struct 104.153240
> Nb2Se3_all_min_mon____6.00.struct 104.153240
> Nb2Se3_all_min_mon____7.00.struct 104.153240
> Nb2Se3_all_min_mon____8.00.struct 104.153240
> Nb2Se3_all_min_mon____9.00.struct 104.153240
> Nb2Se3_all_min.struct 104.153240
>
> [1]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20403.html
> On 8/24/2020 11:25 AM, shamik chakrabarti wrote:
>
> Dear Prof. Laurence Marks Sir,
>
> I have changed the atomic
> coordinates & reduced the symmetry to 1_P with the help of the Bilbao
> crystallographic server. The calculation is still running & 3 structures
> are already generated without showing any error. However, the value of
> Gamma is still not changing. Why so?
>
> Thanks & Regards,
>
> On Mon, 24 Aug 2020 at 18:03, Laurence Marks <laurence.marks at gmail.com>
> wrote:
>
>> You have to also change the positions, and symmetry of course!
>>
>> _____
>> Professor Laurence Marks
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought", Albert Szent-Gyorgi
>> www.numis.northwestern.edu
>>
>> On Mon, Aug 24, 2020, 07:29 shamik chakrabarti <shamik15041981 at gmail.com>
>> wrote:
>>
>>> Dear Prof. Gavin,
>>>
>>> If I change a to b, b to c & c to a to make alpha
>>> to beta, beta to gamma & gamma to alpha the produced structure shows
>>> unphysical RMTs for all the atoms.: 1 for Nb & 0.51 for Se. What to do?
>>>
>>> with regards,
>>>
>>> On Mon, 24 Aug 2020 at 16:07, Gavin Abo <gsabo at crimson.ua.edu> wrote:
>>>
>>>> The 4D is option 7 [
>>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html
>>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvLE6WOCw$>
>>>> ,
>>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html
>>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btgMniYYw$>
>>>> ]:
>>>>
>>>> [7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice)
>>>>
>>>> I think that only worked correctly when the gamma angle was the one
>>>> that was greater than 90 (e.g., in your case it would likely need to be
>>>> alpha=90 degrees, beta = 90 degrees, Gamma=104.15 degrees), refer to:
>>>>
>>>>
>>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html
>>>> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$>
>>>>
>>>>
>>>> On 8/23/2020 11:42 AM, shamik chakrabarti wrote:
>>>>
>>>> Dear wien2k users,
>>>>
>>>> During 4D optimization of a monoclinic system
>>>> (file attached) I have obtained an error as described below;
>>>>
>>>> 'FERMI' - EFERMI OUT OF ENERGY RANGE
>>>> 'FERMI' - STOP IN EFI
>>>> 'FERMI' - ENERGY OF LOWER BOUND : -4.50517
>>>>
>>>> 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND : 0.00000
>>>>
>>>> 'FERMI' - ENERGY OF UPPER BOUND :3003.00451
>>>>
>>>> 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND : 112.00000
>>>>
>>>> 'FERMI' - ADD 112.00000
>>>>
>>>> 'FERMI' - SOS 0.0000.0000.0000.0000.0000.0000.0000.0000.0003.156
>>>>
>>>> 'FERMI' - NOS **************************************************
>>>>
>>>> What is the meaning of this error & how to get out of it?
>>>>
>>>> I have two more queries:
>>>> (1) During 4D optimization, I am also expecting the change in the value
>>>> of Gamma, but it remains the same along with all structures produced by x
>>>> optimize & also in the case_default.struct the Gamma is not changing. why
>>>> so?
>>>>
>>>> (2) In my structure, I have alpha=90 degree, beta = 104.15 degrees,
>>>> Gamma=90 degree. Whether the code will change the beta of my structure or I
>>>> have to change the lattice parameter a to b, b to c & c to a to produce
>>>> alpha to beta, beta to gamma & gamma to alpha?
>>>>
>>>> Looking forward to your reply in this regard. Thanks in advance.
>>>>
>>>> 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
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>>
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>>>
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>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
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> SEARCH the MAILING-LIST at:
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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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