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<p>Dear all, <br>
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<p>I want to do a cell optimization on sodalite (a type of zeolite), however, after I visualize the structure in xcrysden, not only it distorts the whole cell but also the final configuration is very different (not actually sodalite) from its initial one. I
put my input file in case you might need to take a look at. Any help would be thoroughly appreciated.
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<div><span style="color: rgb(0, 111, 201);"><br>
<br>
&CONTROL</span><br>
<span style="color: rgb(0, 111, 201);"> calculation = 'vc-relax' ,</span><br>
<span style="color: rgb(0, 111, 201);"> restart_mode = 'from_scratch' ,</span><br>
<span style="color: rgb(0, 111, 201);"> wf_collect = .true. ,</span><br>
<span style="color: rgb(0, 111, 201);"> outdir = './scratch' ,</span><br>
<span style="color: rgb(0, 111, 201);"> wfcdir = './scratch' ,</span><br>
<span style="color: rgb(0, 111, 201);"> pseudo_dir = '/global/espresso/pseudo' ,</span><br>
<span style="color: rgb(0, 111, 201);"> prefix = 'SOD' ,</span><br>
<span style="color: rgb(0, 111, 201);"> verbosity = 'high' ,</span><br>
<span style="color: rgb(0, 111, 201);"> etot_conv_thr = 1e-5 ,</span><br>
<span style="color: rgb(0, 111, 201);"> forc_conv_thr = 1e-4 ,</span><br>
<span style="color: rgb(0, 111, 201);"> nstep = 50 ,</span><br>
<span style="color: rgb(0, 111, 201);"> tstress = .true. ,</span><br>
<span style="color: rgb(0, 111, 201);"> tprnfor = .true. ,</span><br>
<span style="color: rgb(0, 111, 201);"> /</span><br>
<span style="color: rgb(0, 111, 201);"> &SYSTEM</span><br>
<span style="color: rgb(0, 111, 201);"> ibrav = 0,</span><br>
<span style="color: rgb(0, 111, 201);"> nat = 42,</span><br>
<span style="color: rgb(0, 111, 201);"> ntyp = 4,</span><br>
<span style="color: rgb(0, 111, 201);"> ecutwfc = 50 ,</span><br>
<span style="color: rgb(0, 111, 201);"> ecutrho = 500 ,</span><br>
<span style="color: rgb(0, 111, 201);"> /</span><br>
<span style="color: rgb(0, 111, 201);"> &ELECTRONS</span><br>
<span style="color: rgb(0, 111, 201);"> electron_maxstep = 100,</span><br>
<span style="color: rgb(0, 111, 201);"> conv_thr = 3e-8 ,</span><br>
<span style="color: rgb(0, 111, 201);"> mixing_mode = 'plain' ,</span><br>
<span style="color: rgb(0, 111, 201);"> mixing_beta = 0.7 ,</span><br>
<span style="color: rgb(0, 111, 201);"> diagonalization = 'david' ,</span><br>
<span style="color: rgb(0, 111, 201);"> /</span><br>
<span style="color: rgb(0, 111, 201);"> &IONS</span><br>
<span style="color: rgb(0, 111, 201);"> ion_dynamics = 'bfgs' ,</span><br>
<span style="color: rgb(0, 111, 201);"> trust_radius_ini = 0.5 ,</span><br>
<span style="color: rgb(0, 111, 201);"> /</span><br>
<span style="color: rgb(0, 111, 201);">&CELL</span><br>
<span style="color: rgb(0, 111, 201);"> cell_dynamics = 'bfgs',</span><br>
<span style="color: rgb(0, 111, 201);">/</span><br>
<br>
<span style="color: rgb(0, 111, 201);">CELL_PARAMETERS bohr</span><br>
<span style="color: rgb(0, 111, 201);"> 16.720296750 0.000000000 0.000000000</span><br>
<span style="color: rgb(0, 111, 201);"> 0.000000000 16.720296750 0.000000000</span><br>
<span style="color: rgb(0, 111, 201);"> 0.000000000 0.000000000 16.720296750</span><br>
<br>
<span style="color: rgb(0, 111, 201);">ATOMIC_SPECIES</span><br>
<span style="color: rgb(0, 111, 201);"> Si 28.08600 Si.pbe-n-rrkjus_psl.0.1.UPF</span><br>
<span style="color: rgb(0, 111, 201);"> O 15.99940 O.pbe-n-rrkjus_psl.0.1.UPF</span><br>
<span style="color: rgb(0, 111, 201);"> Al 26.981539 Al.pbe-n-rrkjus_psl.0.1.UPF</span><br>
<span style="color: rgb(0, 111, 201);"> Na 22.989769 Na.pbe-sp-van_ak.UPF</span><br>
<br>
<span style="color: rgb(0, 111, 201);">ATOMIC_POSITIONS angstrom</span><br>
<span style="color: rgb(0, 111, 201);">Si 2.21200 0.00000 4.42400</span><br>
<span style="color: rgb(0, 111, 201);">Si 6.63600 0.00000 4.42400</span><br>
<span style="color: rgb(0, 111, 201);">Si 4.42400 2.21200 0.00000</span><br>
<span style="color: rgb(0, 111, 201);">Si 4.42400 6.63600 0.00000</span><br>
<span style="color: rgb(0, 111, 201);">Si 0.00000 4.42400 2.21200</span><br>
<span style="color: rgb(0, 111, 201);">Si 0.00000 4.42400 6.63600</span><br>
<span style="color: rgb(0, 111, 201);">Al 2.21200 4.42400 0.00000</span><br>
<span style="color: rgb(0, 111, 201);">Al 6.63600 4.42400 0.00000</span><br>
<span style="color: rgb(0, 111, 201);">Al 0.00000 2.21200 4.42400</span><br>
<span style="color: rgb(0, 111, 201);">Al 0.00000 6.63600 4.42400</span><br>
<span style="color: rgb(0, 111, 201);">Al 4.42400 0.00000 2.21200</span><br>
<span style="color: rgb(0, 111, 201);">Al 4.42400 0.00000 6.63600</span><br>
<span style="color: rgb(0, 111, 201);"> O 1.20864 3.83826 1.31835</span><br>
<span style="color: rgb(0, 111, 201);"> O 7.63936 5.00974 1.31835</span><br>
<span style="color: rgb(0, 111, 201);"> O 7.63936 3.83826 7.52965</span><br>
<span style="color: rgb(0, 111, 201);"> O 1.20864 5.00974 7.52965</span><br>
<span style="color: rgb(0, 111, 201);"> O 1.31835 1.20864 3.83826</span><br>
<span style="color: rgb(0, 111, 201);"> O 1.31835 7.63936 5.00974</span><br>
<span style="color: rgb(0, 111, 201);"> O 7.52965 7.63936 3.83826</span><br>
<span style="color: rgb(0, 111, 201);"> O 7.52965 1.20864 5.00974</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.83826 1.31835 1.20864</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.00974 1.31835 7.63936</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.83826 7.52965 7.63936</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.00974 7.52965 1.20864</span><br>
<span style="color: rgb(0, 111, 201);"> O 8.26226 5.63264 5.74235</span><br>
<span style="color: rgb(0, 111, 201);"> O 0.58574 3.21536 5.74235</span><br>
<span style="color: rgb(0, 111, 201);"> O 8.26226 3.21536 3.10565</span><br>
<span style="color: rgb(0, 111, 201);"> O 0.58574 5.63264 3.10565</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.63264 5.74235 8.26226</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.21536 5.74235 0.58574</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.21536 3.10565 8.26226</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.63264 3.10565 0.58574</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.74235 8.26226 5.63264</span><br>
<span style="color: rgb(0, 111, 201);"> O 5.74235 0.58574 3.21536</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.10565 8.26226 3.21536</span><br>
<span style="color: rgb(0, 111, 201);"> O 3.10565 0.58574 5.63264</span><br>
<span style="color: rgb(0, 111, 201);">Na 1.33074 1.33074 1.33074</span><br>
<span style="color: rgb(0, 111, 201);">Na 7.51726 1.33074 7.51726</span><br>
<span style="color: rgb(0, 111, 201);">Na 1.33074 7.51726 7.51726</span><br>
<span style="color: rgb(0, 111, 201);">Na 5.75474 5.75474 5.75474</span><br>
<span style="color: rgb(0, 111, 201);">Na 5.75474 3.09326 3.09326</span><br>
<span style="color: rgb(0, 111, 201);">Na 3.09326 5.75474 3.09326</span><br>
<br>
<br>
<span style="color: rgb(0, 111, 201);">K_POINTS automatic</span><br>
<span style="color: rgb(0, 111, 201);"> 2 2 2 1 1 1</span><br>
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<p>Best,<br>
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<p>Amir M. Mofrad<span> </span></p>
<p>Graduate Research Assistant <span> </span></p>
<p>Chemical Engineering Department</p>
<p>University of Missouri<br>
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