<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Hello all,</span><div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br></div><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></div><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>
<div><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></div><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></div><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></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Here is the vc-relax input code and the error:</div><div><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></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">K_POINTS AUTOMATIC</div></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">
4 4 4 1 1 1</div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px"><div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div>     Error in routine checkallsym (2):</div><div>     not orthogonal operation</div><div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div><div><br></div><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><div><br></div><div>Best,</div><div>Cameron</div></div></div>