[Wien] Space group change during running x sgroup
Peeyush Kumar Kamlesh
peeyush.physik.rku at gmail.com
Sat Jul 25 02:50:58 CEST 2020
Thank you So much Prof. Blaha. It is working now.
On Fri, Jul 24, 2020 at 3:39 PM Peeyush Kumar Kamlesh <
peeyush.physik.rku at gmail.com> wrote:
> 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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