[Wien] Space group change during running x sgroup
Peeyush Kumar Kamlesh
peeyush.physik.rku at gmail.com
Sat Jul 25 02:55:31 CEST 2020
Sir,
One more question. How can I know the space group of the supercell? I
searched but was unable to find it.
Thank you!
On Sat, Jul 25, 2020 at 6:20 AM Peeyush Kumar Kamlesh <
peeyush.physik.rku at gmail.com> wrote:
> 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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