[Wien] Space group change during running x sgroup
Peter Blaha
pblaha at theochem.tuwien.ac.at
Fri Jul 24 12:22:24 CEST 2020
When using w2web, your error is:
> 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
You MUST NOT ignore this question, but should accept it.
With this you finally accept the struct file from nn, and later on you
should NOT accept changes from sgroup.
PS: For such advanced procedures, it is anyway ridiculous to use w2web.
At that point you should already be an "expert" in wien2k and use the
command line (which you have to use anyway a lot for phonopy).
After copying the proper *S-00x.struct file to your case do:
x nn
if an error occurs (usually it will):
cp case.struct_nn case.struct
repeat these 2 lines until nn does not report any error.
x sgroup
x symmetry
Now compare the number of non-equivalent atoms in case.outputsgroup
and case.outputnn
Then compare the number of symmetry operations in case.outputsgroup
and case.outputs. If they agree and no other errors appear in
case.outputs, you are ready to initialize:
init_lapw -b -.... optional options for init_lapw (see init_lapw -h)
run_lapw -fc 0.1 (or better) (-p ...)
> 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 <mailto: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
> <http://RbZnBi.structS-001.in>: 40
> Number of non-equivalent atoms in RbZnBi.structS-002.in
> <http://RbZnBi.structS-002.in>: 38
> Number of non-equivalent atoms in RbZnBi.structS-003.in
> <http://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 <mailto: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
> <mailto: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!
>
>
> _______________________________________________
> Wien mailing list
> Wien at 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
>
--
P.Blaha
--------------------------------------------------------------------------
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: blaha at theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at/TC_Blaha
--------------------------------------------------------------------------
More information about the Wien
mailing list