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<div>Hi Cameron,</div>
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<div>I’m a relatively new user of PWscf, but I’ll take a try to help you out. I see two potential problems with your setup:</div>
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<li>I’m not sure that you have the correct ATOMIC_POSITIONS and CELL_PARAMETERS, especially for the ibrav=2 structure type. If you examine the online documentation (<a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html">http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html</a>),
you’ll notice that the lattice directions are not the <100>/cubic directions (ibrav=1), but rather <110>-type directions. Thus, I’m not sure that the values you’ve listed are correct. In particular, it’s odd that a few of your CELL_PARAMETERS values are negative.
I’m not sure what that’s supposed to mean.</li><li>Secondly, I believe the ‘2Dxy’ specification for cell_dofree is opposite to your intent. I believe you want to specify, and then fix during relaxation, the x-y dimensions of your system and only allow z to change. If that’s the case, then the correct option
would be cell_dofree=z.</li></ol>
<div>Good luck,</div>
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<div>Jon Zimmerman</div>
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<span style="font-weight:bold">From: </span>Cameron Foss <<a href="mailto:cjfoss@umass.edu">cjfoss@umass.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, August 14, 2014 at 2:28 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
<span style="font-weight:bold">Subject: </span>[EXTERNAL] [Pw_forum] Biaxial Strian Silicon<br>
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<div dir="ltr"><span style="font-family: arial, sans-serif; font-size: 12.727272033691406px;">Hello all,</span>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">I am trying to study phonons in silicon under biaxial strain, which occurs when you grow thin films of silicon over a germanium(or SiGe) bulk, which has a slightly larger lattice constant
than silicon, thus stretching the silicon out. This type of procedure stretches silicon in the xy directions and slightly compresses it in the z direction. This consequently distorts the symmetry of the crystal.</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">I have ran some strained cases; in which I "strain" the crystal by changing the lattice vectors in the CELL_PARAMETERS CARD and the atomic positions like so:</div>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">ATOMIC_POSITIONS {alat}</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Si 0 0 0</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Si 0.255 0.255 0.25</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">CELL_PARAMETERS {alat}</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"> -0.51 0.00 0.5</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"> 0.00 0.51 0.5</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"> -0.51 0.51 0.00</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Whilst the lattice constant remained the equilibrium lattice constant 5.431Angs.</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">However, I would like to use the vc-relax calculation to relax the structure to the strained amount...so I know that the structure is optimized. Although I keep getting an orthogonal operation
error.</div>
<div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Here is the vc-relax input code and the error:</div>
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<div style=""><font face="arial,sans-serif">&control</font></div>
<div style=""><font face="arial,sans-serif"> calculation='vc-relax'</font></div>
<div style=""><font face="arial,sans-serif"> restart_mode='from_scratch',</font></div>
<div style=""><font face="arial,sans-serif"> outdir='/home/cameron/QE/espresso-5.1/wktmp',</font></div>
<div style=""><font face="arial,sans-serif"> pseudo_dir='/home/cameron/QE/espresso-5.1/pseudo',</font></div>
<div style=""><font face="arial,sans-serif"> prefix='relax'</font></div>
<div style=""><font face="arial,sans-serif">/</font></div>
<div style=""><font face="arial,sans-serif">&system</font></div>
<div style=""><font face="arial,sans-serif"> ibrav=2, celldm(1)=10.263, nat=2, ntyp=1,</font></div>
<div style=""><font face="arial,sans-serif"> ecutwfc =24.0</font></div>
<div style=""><font face="arial,sans-serif">/</font></div>
<div style=""><font face="arial,sans-serif">&electrons</font></div>
<div style=""><font face="arial,sans-serif"> conv_thr = 1.0d-10</font></div>
<div style=""><font face="arial,sans-serif"> mixing_beta = 0.4</font></div>
<div style=""><font face="arial,sans-serif">/</font></div>
<div style=""><font face="arial,sans-serif">&ions</font></div>
<div style=""><font face="arial,sans-serif"> ion_dynamics='damp'</font></div>
<div style=""><font face="arial,sans-serif">/</font></div>
<div style=""><font face="arial,sans-serif">&cell</font></div>
<div style=""><font face="arial,sans-serif"> cell_dynamics='damp-w',</font></div>
<div style=""><font face="arial,sans-serif"> press=55.0,</font></div>
<div style=""><font face="arial,sans-serif"> cell_dofree='2Dxy'</font></div>
<div style=""><font face="arial,sans-serif">/</font></div>
<div style=""><font face="arial,sans-serif">ATOMIC_SPECIES</font></div>
<div style=""><font face="arial,sans-serif"> Si 28.0855 Si.pz-vbc.UPF</font></div>
<div style=""><font face="arial,sans-serif">ATOMIC_POSITIONS</font></div>
<div style=""><font face="arial,sans-serif"> Si 0.00 0.00 0.00</font></div>
<div style=""><font face="arial,sans-serif"> Si 0.25 0.25 0.25</font></div>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">K_POINTS AUTOMATIC</div>
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<div style="font-family:arial,sans-serif;font-size:12.727272033691406px">4 4 4 1 1 1</div>
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<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div> Error in routine checkallsym (2):</div>
<div> not orthogonal operation</div>
<div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
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<div>I have two main questions: Did I incorrectly manually "strain" the lattice structure in the first case? </div>
<div>And how can I use/fix the vc-relax code to simulate the strained structure?</div>
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<div>Best,</div>
<div>Cameron</div>
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