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Hey Israel,
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<div>Check the struct file for the supercell.</div>
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<div>Did you change the Z as well as the atom? Remember the atom number Z is set automatically by ``set RMT and continue editing'', but once it is set (to 34 for Se, for example) you will need to change it manually.</div>
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<div>So if you relabel an Se atom as Te, you also need to change the Z to 52.</div>
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<div>-John</div>
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<div>On 2013-08-20, at 9:08 PM, Israel Pérez wrote:</div>
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<div>Hi Prof. P. Blaha</div>
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<div style="color: rgb(0, 0, 0); font-size: 13px; background-color: transparent; font-style: normal; ">
I need some help with supercell calculations. I'd like to investigate the effect of replacing Se with Te in the system FeSe. Structure file is as shown below. </div>
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<div style="color: rgb(0, 0, 0); font-size: 13px; background-color: transparent; font-style: normal; ">
FeSe </div>
<div>P LATTICE,NONEQUIV.ATOMS: 2129_P4/nmm </div>
<div>MODE OF CALC=RELA unit=ang </div>
<div> 7.119735 7.119735 10.364585 90.000000 90.000000 90.000000 </div>
<div>ATOM -1: X=0.25000000 Y=0.75000000 Z=0.00000000</div>
<div> MULT= 2 ISPLIT=-2</div>
<div> -1: X=0.75000000 Y=0.25000000 Z=0.00000000</div>
<div>Fe NPT= 781 R0=0.00005000 RMT= 2.1900 Z: 26.0 </div>
<div>LOCAL ROT MATRIX: 0.7071068-0.7071068 0.0000000</div>
<div> 0.7071068 0.7071068 0.0000000</div>
<div> 0.0000000 0.0000000 1.0000000</div>
<div>ATOM -2: X=0.25000000 Y=0.25000000 Z=0.23720000</div>
<div> MULT= 2 ISPLIT=-2</div>
<div> -2: X=0.75000000 Y=0.75000000 Z=0.76280000</div>
<div>Se NPT= 781 R0=0.00005000 RMT= 1.9400 Z: 34.0 </div>
<div>LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000</div>
<div> 0.0000000 1.0000000 0.0000000</div>
<div> 0.0000000 0.0000000 1.0000000</div>
<div> 16 NUMBER OF SYMMETRY OPERATIONS</div>
<div>-1 0 0 0.00000000</div>
<div> 0-1 0 0.00000000</div>
<div> 0 0-1 0.00000000</div>
<div> 1</div>
<div> 0-1 0 0.00000000</div>
<div>-1 0 0 0.00000000</div>
<div> 0 0-1 0.00000000</div>
<div> 2</div>
<div> 0 1 0 0.00000000</div>
<div> 1 0 0 0.00000000</div>
<div> 0 0 1 0.00000000</div>
<div> 3</div>
<div> 1 0 0 0.00000000</div>
<div> 0 1 0 0.00000000</div>
<div> 0 0 1 0.00000000</div>
<div> 4</div>
<div>-1 0 0 0.50000000</div>
<div> 0 1 0 0.00000000</div>
<div> 0 0 1 0.00000000</div>
<div> 5</div>
<div>-1 0 0 0.50000000</div>
<div> 0-1 0 0.50000000</div>
<div> 0 0 1 0.00000000</div>
<div> 6</div>
<div> 0-1 0 0.50000000</div>
<div>-1 0 0 0.50000000</div>
<div> 0 0 1 0.00000000</div>
<div> 7</div>
<div> 0 1 0 0.50000000</div>
<div>-1 0 0 0.00000000</div>
<div> 0 0-1 0.00000000</div>
<div> 8</div>
<div> 0 1 0 0.00000000</div>
<div>-1 0 0 0.50000000</div>
<div> 0 0 1 0.00000000</div>
<div> 9</div>
<div> 0-1 0 0.00000000</div>
<div> 1 0 0 0.50000000</div>
<div> 0 0-1 0.00000000</div>
<div> 10</div>
<div> 0-1 0 0.50000000</div>
<div> 1 0 0 0.00000000</div>
<div> 0 0 1 0.00000000</div>
<div> 11</div>
<div> 0 1 0 0.50000000</div>
<div> 1 0 0 0.50000000</div>
<div> 0 0-1 0.00000000</div>
<div> 12</div>
<div>-1 0 0 0.00000000</div>
<div> 0 1 0 0.50000000</div>
<div> 0 0-1 0.00000000</div>
<div> 13</div>
<div> 1 0 0 0.50000000</div>
<div> 0-1 0 0.00000000</div>
<div> 0 0-1 0.00000000</div>
<div> 14</div>
<div> 1 0 0 0.00000000</div>
<div> 0-1 0 0.50000000</div>
<div> 0 0 1 0.00000000</div>
<div> 15</div>
<div> 1 0 0 0.50000000</div>
<div> 0 1 0 0.50000000</div>
<div> 0 0-1 0.00000000</div>
<div> 16</div>
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<div>Then I copy it to a new session and create a supercell 2X2X1 with lattice F. T<span style="font-size: 10pt; ">he program recognizes 8 inequivalent atoms, each with two positions (total of 16 atoms). Then I replace the last atom of Se by Te so that I have
a doping of 25% and set its RMT to 2 and the atomic number to 52. RMT_Fe=2.1 and RMT_Se=1.96. Here I have a couple of questions. First, I wonder if we have to label all inequivalent atoms (for instance, Fe1, Fe2, Se1, Se2, etc.) because when I compute xnn,
I got a warning like this</span></div>
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<pre style="font-size: 16px; background-color: rgb(240, 240, 240); "> WARNING: Mult not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
WARNING: ityp not equal. PLEASE CHECK outputnn-file
NN created a new SFeSeTe.struct_nn file
NN created a new CASE.STRUCT_NN FILE
0.016u 0.000s 0:00.01 100.0% 0+0k 0+160io 0pf+0w</pre>
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<div style="font-size: 10pt; "></div>
<div style="font-size: 10pt; ">If I continue to x group I got another warning such as this:</div>
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<div style="font-size: 10pt; "><span style="font-size: medium; background-color: rgb(255, 169, 169); ">warning: !!! Number of inequivalent atoms has changed. !!! Old value= 8 New value= 6 warning: !!! Bravais lattice has changed.</span><br style="font-size: medium; ">
<span style="font-size: 16px; background-color: rgb(255, 169, 169); ">sgroup found: 12 (C 2/m) [unique axis c] cell choice 2</span><br>
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<div style="font-size: 10pt; ">Why? And then the program suggests to change the sgroup. If I don't accept and continue I get an error in editinst step: </div>
<div style="font-size: 10pt; "><span style="background-color: rgb(255, 169, 169); font-size: 16px;
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<div style="font-size: 10pt; "><span style="background-color: rgb(255, 169, 169); font-size: 16px; ">error: SFeSeTe.inst not consistent with Z</span></div>
<span style="font-size: 16px; background-color: rgb(255, 169, 169); ">edit SFeSeTe.inst and rerun lstart afterwards or change Z in StructGen!</span>
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<div><font>On the other hand, if I labeled the atoms, the warnings after xnn is executed don't appear anymore. However, when I run sgroup, I got a warning:</font></div>
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<span style="background-color: rgb(255, 169, 169); ">warning: !!! Struct file is not consistent with space group found. </span><br>
<div><font><span style="background-color: rgb(255, 169, 169); ">sgroup found: !!! Struct file is not consistent with space group found. Number and name of space group: 2 (P -1)</span></font></div>
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<div><font>which causes errors in forthcoming steps. Should I labeled them and why? What is the correct procedure to avoid these warnings and perform supercell calculations successfully. I'm a beginner with supercell calculations.</font></div>
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<div><font>I have already read the manual but the information is not enough to solve this problem. I also checked the wien list of problems. There are some similar to mine but the warnings and errors are different. I'd appreciate any assistance you may have. </font></div>
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<div><font>Regards</font></div>
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<div><font>Thanks</font></div>
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<div><span style="font-family: verdana, helvetica, sans-serif; font-size: 13px; ">Israel Perez</span>
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