Thank you So much Prof. Blaha. It is working now.
On Fri, Jul 24, 2020 at 3:39 PM Peeyush Kumar Kamlesh < [email protected]> 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 < > [email protected]> 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 < >> [email protected]> 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 < >>> [email protected]> 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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