[Wien] Space group change during running x sgroup
Peeyush Kumar Kamlesh
peeyush.physik.rku at gmail.com
Fri Jul 24 12:09:00 CEST 2020
Sir,
Output of x nn is:
-----------------------------------------
specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about
1.d-5, 20)]
DSTMAX: 30.2976897600000
iix,iiy,iiz 2 2 2 54.5904320000000
54.5904320000000 54.5904320000000
ATOM 1 Rb ATOM 41 Zn
RMT( 1)=2.50000 AND RMT( 41)=2.50000
SUMS TO 5.00000 LT. NN-DIST= 5.89806
And so on till
ATOM 96 Bi ATOM 40 Zn
RMT( 96)=2.50000 AND RMT( 40)=2.50000
SUMS TO 5.00000 LT. NN-DIST= 5.90959
WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: Mult not equal. PLEASE CHECK outputnn-file
--------------------------------------------
When I ignore this warning and accept the changes produced by nn, then it
pops up a new question (Use new struct-file?). on clicking on YES, it
Displays a message:
*Case-001.struct_nn copied to case-001.struct old struct-file saved as
case-001.struct_init case-001.inst updated*
And ask to start StructGen again.
On ignoring this question, when I click on x sgroup, it shows following
warning:
*warning: !!! Number of inequivalent atoms has changed. !!! Old value= 34
New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35 (C
m m 2) Note that shift vectors for this space group are defined.*
On further proceeding, it reflects an error in dstart;-
*ROTDEF - Error
0.0u 0.0s 0:00.68 4.4% 0+0k 29488+24io 82pf+0w*
On the contrary, if I agree on start StructGen again, and run x sgroup then
it again show the following warning:
*warning: !!! Number of inequivalent atoms has changed. !!! Old value= 96
New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35 (C
m m 2) Note that shift vectors for this space group are defined.*
*warning: !!! Bravais lattice has changed.*
And ask to accept a new file generated by sgroup. When I accept it then in
further process, it does not show any error.
But in the Phonopy manual it has been written that, *"Calculate forces on
atoms in the supercells with displacements. It is necessary to use
case.struct_nn file when running init_lapw. Note that case.struct_sgroup
file can’t be used with phonopy."*
*I am confused, how should I proceed further?*
Thank you!
On Fri, Jul 24, 2020 at 11:56 AM Peeyush Kumar Kamlesh <
peeyush.physik.rku at gmail.com> wrote:
> Dear Blaha Sir,
> 1. First I prepared a case.struct file with optimized lattice parameters,
> having F43m spacegroup (216). Which F lattice. it is as follows:
> ----------------------------------------------------------
>
> F LATTICE,NONEQUIV.ATOMS: 3 216_F-43m
> MODE OF CALC=RELA unit=ang
> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000
> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000
> MULT= 1 ISPLIT= 2
> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> ATOM 2: X=0.25000000 Y=0.25000000 Z=0.25000000
> MULT= 1 ISPLIT= 2
> Zn NPT= 781 R0=0.00005000 RMT= 2.5000 Z: 30.000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> ATOM 3: X=0.00000000 Y=0.00000000 Z=0.00000000
> MULT= 1 ISPLIT= 2
> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 24 NUMBER OF SYMMETRY OPERATIONS
>
> ------------------------------------------------------------------------------------
> 2. Then I created a supercell (1x1x1) using wien2k, having P lattice but
> with the same space group. case_super .struct file is as follows:
> -----------------------------------------------------------
>
> P LATTICE,NONEQUIV. ATOMS 12
> MODE OF CALC=RELA unit=ang
> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000
> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000
> MULT= 1 ISPLIT= 2
> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.0
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> And so on ................. till
> ATOM 12: X=0.00000000 Y=0.50000000 Z=0.50000000
> MULT= 1 ISPLIT= 2
> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.0
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 0 NUMBER OF SYMMETRY OPERATIONS
> -------------------------------------------------------------
> 3. Then I copied case_super.struct to case.struct file and used the
> command (phonopy --wien2k -d --dim="2 2 2" -c case.struct) to run phonopy
> with a supercell of (2x2x2). its output is as follows:
> ---------------------------------------------------
> _
> _ __ | |__ ___ _ __ ___ _ __ _ _
> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
> | |_) | | | | (_) | | | | (_) || |_) | |_| |
> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
> |_| |_| |___/
> 2.7.0
>
> Python version 3.8.4
> Spglib version 1.15.1
>
> Calculator interface: wien2k
> Crystal structure was read from "RbZnBi.struct".
> Unit of length: au
> Displacements creation mode
> Settings:
> Supercell: [2 2 2]
> Spacegroup: F-43m (216)
> Use -v option to watch primitive cell, unit cell, and supercell structures.
>
> Number of non-equivalent atoms in RbZnBi.structS-001.in: 40
> Number of non-equivalent atoms in RbZnBi.structS-002.in: 38
> Number of non-equivalent atoms in RbZnBi.structS-003.in: 40
> "phonopy_disp.yaml" and supercells have been created.
>
> Summary of calculation was written in "phonopy_disp.yaml".
> _
> ___ _ __ __| |
> / _ \ '_ \ / _` |
> | __/ | | | (_| |
> \___|_| |_|\__,_|
> ------------------------------------------------------------------------
>
> 4. It is clear from the output that the space group is not changed. It
> generates one file for a perfect supercell and 3 files (case-xxx.struct)
> for supercells with displacements. case-xxx.struct is as follows:
> ---------------------------------------------------
> Title
> P LATTICE,NONEQUIV.ATOMS: 96
> MODE OF CALC=RELA
> 27.295216 27.295216 27.295216 90.000000 90.000000 90.000000
> ATOM -1: X=0.25073273 Y=0.25000000 Z=0.25000000
> MULT= 1 ISPLIT= 8
> Rb NPT= 781 R0=0.00001000 RMT= 2.50000 Z: 37.0
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> And so on.........till
> ATOM -96: X=0.50000000 Y=0.75000000 Z=0.75000000
> MULT= 1 ISPLIT= 8
> Bi NPT= 781 R0=0.00000500 RMT= 3.0000 Z: 83.000
> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
> 0.0000000 1.0000000 0.0000000
> 0.0000000 0.0000000 1.0000000
> 0 NUMBER OF SYMMETRY OPERATIONS
>
> --------------------------------------------------------------------------------------
> 5. Then I picked one of the case-xxx.struct files and put in another
> directory for initialization and started step by step initialization. and
> perform x nn: Which Shows following warning:
>
> WARNING: Mult not equal. PLEASE CHECK outputnn-file
> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>
> 6. Then I tried to increase RMT up 3. It now shows the following message:
> ERROR !!!!!!!!!!!!!!!
> RMT( 1)=3.00000 AND RMT( 41)=3.00000
> SUMS TO 6.00000 GT NNN-DIST= 5.89806
> WARNING: Mult not equal. PLEASE CHECK outputnn-file
> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>
> Please suggest What should I do? I shall be grateful to you!
>
> Thanks and Regards
>
>
> On Fri, Jul 24, 2020 at 1:53 AM Peeyush Kumar Kamlesh <
> peeyush.physik.rku at gmail.com> wrote:
>
>> Before that when I run the command x nn, it shows following error:
>>
>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>>
>> I have tried by putting different values for nn, but it is not changing.
>>
>> What will be its solution?
>>
>>
>> On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh <
>> peeyush.physik.rku at gmail.com> wrote:
>>
>>> Dear Wien2k users,
>>> Greetings!
>>> I am working on XYZ half-Heusler compounds with space group no.-216.
>>> When I do initialization of a struct file of a supercell. then output of x
>>> sgroup shows some warning:
>>>
>>> warning: !!! Number of inequivalent atoms has changed. !!! Old value= 34
>>> New value= 40 warning: !!! Bravais lattice has changed.
>>> sgroup found: 35 (C m m 2) Note that shift vectors for this space group
>>> are defined.
>>> Bravais lattice: Orthorhombic C-base centred.
>>> Kindly help me to solve the problem.
>>>
>>> Thank you!
>>>
>>
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