<div dir="ltr"><div dir="ltr"><div>Thank you So much Prof. Blaha. It is working now.</div><div><br></div><br><div><br></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 24, 2020 at 3:39 PM Peeyush Kumar Kamlesh <<a href="mailto:peeyush.physik.rku@gmail.com">peeyush.physik.rku@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Sir,</div><div>Output of x nn is:</div><div>-----------------------------------------</div><div><pre>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<br><br>And so on till <br><br>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</pre><pre>--------------------------------------------<br></pre></div><div>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:</div><div><b>Case-001.struct_nn copied to case-001.struct<br>
old struct-file saved as case-001.struct_init<br>
case-001.inst updated</b></div><div>And ask to start StructGen again.</div><div>On ignoring this question, when I click on x sgroup, it shows following warning:</div><div><font size="2"><span style="font-family:arial,sans-serif"><b>warning: !!! Number of inequivalent atoms has changed.
!!! Old value= 34 New value= 40
warning: !!! Bravais lattice has changed.
<br>sgroup found: 35 (C m m 2)
Note that shift vectors for this space group are defined.</b></span></font></div><font size="2">On further proceeding<span style="font-family:arial,sans-serif">, it reflects an error in dstart;- <br></span></font><pre><b><span style="font-family:arial,sans-serif">ROTDEF - Error
0.0u 0.0s 0:00.68 4.4% 0+0k 29488+24io 82pf+0w</span></b></pre><div>On the contrary, if I agree on start StructGen again, and run x sgroup then it again show the following warning:</div><div><b><font size="2"><span style="font-family:arial,sans-serif">warning: !!! Number of inequivalent atoms has changed.
!!! Old value= 96 New value= 40
warning: !!! Bravais lattice has changed.
<br>sgroup found: 35 (C m m 2)
Note that shift vectors for this space group are defined.</span></font></b></div><div><b><font size="2"><span style="font-family:arial,sans-serif">warning: !!! Bravais lattice has changed.</span></font></b></div><div><font size="2"><span style="font-family:arial,sans-serif">And ask to accept a new file generated by sgroup. When I accept it then in further process, it does not show any error.</span></font></div><div><font size="2"><span style="font-family:arial,sans-serif"><br></span></font></div><div><font size="2"><span style="font-family:arial,sans-serif">But in the Phonopy manual it has been written that, <b>"Calculate forces on atoms in the supercells with displacements. It
is necessary to use <code><span>case.struct_nn</span></code> file when running
<code><span>init_lapw</span></code>. Note that <code><span>case.struct_sgroup</span></code> file can’t be used
with phonopy."</b></span></font></div><div><font size="2"><span style="font-family:arial,sans-serif"><b><br></b></span></font></div><div><font size="2"><span style="font-family:arial,sans-serif"><b>I am confused, how should I proceed further?</b></span></font></div><div><font size="2"><span style="font-family:arial,sans-serif"><b><br></b></span></font></div><div><font size="2"><span style="font-family:arial,sans-serif">Thank you!<br>
</span></font></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 24, 2020 at 11:56 AM Peeyush Kumar Kamlesh <<a href="mailto:peeyush.physik.rku@gmail.com" target="_blank">peeyush.physik.rku@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear Blaha Sir,</div><div>1. First I prepared a case.struct file with optimized lattice parameters, having F43m spacegroup (216). Which F lattice. it is as follows:</div><div>---------------------------------------------------------- <br>F LATTICE,NONEQUIV.ATOMS: 3 216_F-43m <br>MODE OF CALC=RELA unit=ang <br> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000<br>ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000<br> MULT= 1 ISPLIT= 2<br>Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.000<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br>ATOM 2: X=0.25000000 Y=0.25000000 Z=0.25000000<br> MULT= 1 ISPLIT= 2<br>Zn NPT= 781 R0=0.00005000 RMT= 2.5000 Z: 30.000<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br>ATOM 3: X=0.00000000 Y=0.00000000 Z=0.00000000<br> MULT= 1 ISPLIT= 2<br>Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.000<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000</div><div>24 NUMBER OF SYMMETRY OPERATIONS</div><div>------------------------------------------------------------------------------------<br></div><div>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:</div><div>----------------------------------------------------------- <br>P LATTICE,NONEQUIV. ATOMS 12 <br>MODE OF CALC=RELA unit=ang <br> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000<br>ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000<br> MULT= 1 ISPLIT= 2<br>Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.0<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br></div><div>And so on ................. till<br></div><div>ATOM 12: X=0.00000000 Y=0.50000000 Z=0.50000000<br> MULT= 1 ISPLIT= 2<br>Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.0<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br> 0 NUMBER OF SYMMETRY OPERATIONS</div><div>-------------------------------------------------------------<br></div><div>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:</div><div>---------------------------------------------------</div><div> _<br> _ __ | |__ ___ _ __ ___ _ __ _ _<br> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |<br> | |_) | | | | (_) | | | | (_) || |_) | |_| |<br> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |<br> |_| |_| |___/<br> 2.7.0<br><br>Python version 3.8.4<br>Spglib version 1.15.1<br><br>Calculator interface: wien2k<br>Crystal structure was read from "RbZnBi.struct".<br>Unit of length: au<br>Displacements creation mode<br>Settings:<br> Supercell: [2 2 2]<br>Spacegroup: F-43m (216)<br>Use -v option to watch primitive cell, unit cell, and supercell structures.<br><br>Number of non-equivalent atoms in <a href="http://RbZnBi.structS-001.in" target="_blank">RbZnBi.structS-001.in</a>: 40<br>Number of non-equivalent atoms in <a href="http://RbZnBi.structS-002.in" target="_blank">RbZnBi.structS-002.in</a>: 38<br>Number of non-equivalent atoms in <a href="http://RbZnBi.structS-003.in" target="_blank">RbZnBi.structS-003.in</a>: 40<br>"phonopy_disp.yaml" and supercells have been created.<br><br>Summary of calculation was written in "phonopy_disp.yaml".<br> _<br> ___ _ __ __| |<br> / _ \ '_ \ / _` |<br> | __/ | | | (_| |<br> \___|_| |_|\__,_|<br></div><div>------------------------------------------------------------------------<br></div><div><br></div><div>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:</div><div>---------------------------------------------------</div><div>Title<br>P LATTICE,NONEQUIV.ATOMS: 96<br>MODE OF CALC=RELA<br> 27.295216 27.295216 27.295216 90.000000 90.000000 90.000000<br>ATOM -1: X=0.25073273 Y=0.25000000 Z=0.25000000<br> MULT= 1 ISPLIT= 8<br>Rb NPT= 781 R0=0.00001000 RMT= 2.50000 Z: 37.0<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br>And so on.........till<br>ATOM -96: X=0.50000000 Y=0.75000000 Z=0.75000000<br> MULT= 1 ISPLIT= 8<br>Bi NPT= 781 R0=0.00000500 RMT= 3.0000 Z: 83.000<br>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000<br> 0.0000000 1.0000000 0.0000000<br> 0.0000000 0.0000000 1.0000000<br> 0 NUMBER OF SYMMETRY OPERATIONS</div><div>--------------------------------------------------------------------------------------<br></div><div>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:</div><div><pre><span style="font-family:arial,sans-serif"> 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:<br>ERROR !!!!!!!!!!!!!!!
RMT( 1)=3.00000 AND RMT( 41)=3.00000
SUMS TO 6.00000 GT NNN-DIST= 5.89806<br>WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file<br><br></span></pre><pre><span style="font-family:arial,sans-serif">Please suggest What should I do? I shall be grateful to you!<br><br></span></pre><pre><span style="font-family:arial,sans-serif">Thanks and Regards<br></span></pre></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 24, 2020 at 1:53 AM Peeyush Kumar Kamlesh <<a href="mailto:peeyush.physik.rku@gmail.com" target="_blank">peeyush.physik.rku@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><font size="2"><span style="font-family:arial,sans-serif">Before that when I run the command x nn, it shows following error:</span></font></div><div><pre><font size="2"><span style="font-family:arial,sans-serif">WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file<br><br></span></font></pre><pre><font size="2"><span style="font-family:arial,sans-serif">I have tried by putting different values for nn, but it is not changing.<br></span></font></pre><pre><font size="2"><span style="font-family:arial,sans-serif">What will be its solution?</span></font><br></pre></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh <<a href="mailto:peeyush.physik.rku@gmail.com" target="_blank">peeyush.physik.rku@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear Wien2k users,</div><div>Greetings!</div><div>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:</div><div><br></div><div><font size="2"><span style="font-family:arial,sans-serif">warning: !!! Number of inequivalent atoms has changed.
!!! Old value= 34 New value= 40
warning: !!! Bravais lattice has changed.
<br>sgroup found: 35 (C m m 2)
Note that shift vectors for this space group are defined.</span></font></div><div><font size="2"><span style="font-family:arial,sans-serif">Bravais lattice: Orthorhombic C-base centred.</span></font></div><div><font size="2"><span style="font-family:arial,sans-serif">Kindly help me to solve the problem.</span></font></div><div><small><font size="2"><span style="font-family:arial,sans-serif"><br></span></font></small></div><div><small><font size="2"><span style="font-family:arial,sans-serif">Thank you!</span></font><br></small></div></div>
</blockquote></div>
</blockquote></div>
</blockquote></div>
</blockquote></div></div>