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....@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....@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....@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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