<div dir="ltr"><div>Hi Zhendong,</div><div> </div><div>Thanks for your suggestion! </div><div> </div><div>I tried without fixing the atom for Si2, and the geometry is </div><div> </div><div><span lang="EN"><p> i = 20, E = -7.6373030835</p>
<p> Si 2.7020961928 0.9317906628 1.3251881238</p>
<p> Si 0.0002037244 0.6283827813 -0.2219791667</p><p>And the cell structure given by</p><span lang="EN"><p> CELL| Volume [angstrom^3]: 111.629</p><p> CELL| Vector a [angstrom]: 5.405 0.000 0.000 |a| = 5.405</p><p> CELL| Vector b [angstrom]: 2.702 4.681 0.000 |b| = 5.405</p><p> CELL| Vector c [angstrom]: 2.702 1.560 4.413 |c| = 5.405</p><p> CELL| Angle (b,c), alpha [degree]: 60.000</p><p> CELL| Angle (a,c), beta [degree]: 60.000</p><p> CELL| Angle (a,b), gamma [degree]: 60.000</p><p> CELL| Requested initial symmetry: RHOMBOHEDRAL</p><p> CELL| Numerically orthorhombic: NO</p><p>It seems that the bond length is still far too long.</p><p>Any other thoughts on this from you all?</p></span><p> </p></span><br>On Friday, February 6, 2015 at 11:14:44 AM UTC-4, Du Zhang wrote:</div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;"><div dir="ltr"><div>Hi Everyone,</div><div> </div><div>I ran into some confusing results when I attempted to perform the following geometry optimizations on Si crystal with Si2 and Si8 unit cells. </div><div> </div><div>The input file for Si2:</div><div> </div><span lang="EN"><p>&GLOBAL</p><div>
</div><p> PROJECT Si_bulk2</p><div>
</div><p> RUN_TYPE CELL_OPT</p><div>
</div><p> PRINT_LEVEL MEDIUM</p><div>
</div><p>&END GLOBAL</p><div>
</div><p>&FORCE_EVAL</p><div>
</div><p> METHOD Quickstep</p><div>
</div><p> STRESS_TENSOR ANALYTICAL</p><div>
</div><p> &SUBSYS</p><div>
</div><p> &KIND Si</p><div>
</div><p> ELEMENT Si</p><div>
</div><p> BASIS_SET DZVP-GTH-PADE</p><div>
</div><p> POTENTIAL GTH-PADE-q4</p><div>
</div><p> &END KIND</p><div>
</div><p> &CELL</p><div>
</div><p> A 3.83753393 0.00000000 0.00000000</p><div>
</div><p> B 1.91876697 3.32340187 0.00000000</p><div>
</div><p> C 1.91876697 1.10780062 3.13333333</p><div>
</div><p> SYMMETRY RHOMBOHEDRAL</p><div>
</div><p> PERIODIC XYZ</p><div>
</div><p> &END CELL</p><div>
</div><p> &COORD</p><div>
</div><p> Si 1.91876697 1.10780062 0.78333333</p><div>
</div><p> Si 0.00000000 -0.00000000 -0.00000000</p><div>
</div><p> &END COORD</p><div>
</div><p> &END SUBSYS</p><div>
</div><p> &DFT</p><div>
</div><p> BASIS_SET_FILE_NAME BASIS_SET</p><div>
</div><p> POTENTIAL_FILE_NAME GTH_POTENTIALS</p><div>
</div><p> &QS</p><div>
</div><p> EPS_DEFAULT 1.0E-10</p><div>
</div><p> &END QS</p><div>
</div><p> &MGRID</p><div>
</div><p> NGRIDS 4</p><div>
</div><p> CUTOFF 300</p><div>
</div><p> REL_CUTOFF 60</p><div>
</div><p> &END MGRID</p><div>
</div><p> &XC</p><div>
</div><p> &XC_FUNCTIONAL PADE</p><div>
</div><p> &END XC_FUNCTIONAL</p><div>
</div><p> &END XC</p><div>
</div><p> &SCF</p><div>
</div><p> SCF_GUESS ATOMIC</p><div>
</div><p> EPS_SCF 1.0E-7</p><div>
</div><p> MAX_SCF 300</p><div>
</div><p> ADDED_MOS 10</p><div>
</div><p> &DIAGONALIZATION ON</p><div>
</div><p> ALGORITHM STANDARD</p><div>
</div><p> &END DIAGONALIZATION</p><div>
</div><p> &MIXING T</p><div>
</div><p> METHOD BROYDEN_MIXING</p><div>
</div><p> ALPHA 0.4</p><div>
</div><p> NBROYDEN 8</p><div>
</div><p> &END MIXING</p><div>
</div><p> &SMEAR ON</p><div>
</div><p> METHOD FERMI_DIRAC</p><div>
</div><p> ELECTRONIC_TEMPERATURE [K] 300</p><div>
</div><p> &END SMEAR</p><div>
</div><p> &END SCF</p><div>
</div><p> &END DFT</p><div>
</div><p> &PRINT</p><div>
</div><p> &FORCES ON</p><div>
</div><p> &END FORCES</p><div>
</div><p> &END PRINT</p><div>
</div><p>&END FORCE_EVAL</p><div>
</div><p>&MOTION</p><div>
</div><p> &CELL_OPT</p><div>
</div><p> KEEP_ANGLES</p><div>
</div><p> KEEP_SYMMETRY</p><div>
</div><p> &END CELL_OPT</p><div>
</div><p> &GEO_OPT</p><div>
</div><p> TYPE MINIMIZATION</p><div>
</div><p> MAX_DR 1.0E-03</p><div>
</div><p> MAX_FORCE 1.0E-03</p><div>
</div><p> RMS_DR 1.0E-03 </p><div>
</div><p> RMS_FORCE 1.0E-03</p><div>
</div><p> MAX_ITER 200</p><div>
</div><p> OPTIMIZER BFGS</p><div>
</div><p> !&BFGS</p><div>
</div><p> ! MAX_STEEP_STEPS 0</p><div>
</div><p> ! RESTART_LIMIT 9.0E-01</p><div>
</div><p> !&END BFGS</p><div>
</div><p> &END GEO_OPT</p><div>
</div><p> &CONSTRAINT</p><div>
</div><p> &FIXED_ATOMS</p><div>
</div><p> COMPONENTS_TO_FIX XYZ</p><div>
</div><p> LIST 2</p><div>
</div><p> &END FIXED_ATOMS</p><div>
</div><p> &END CONSTRAINT</p><div>
</div><p>&END MOTION </p><p>Its initial cell structure is given by:</p><span lang="EN"><p> CELL| Volume [angstrom^3]: 39.961</p><p> CELL| Vector a [angstrom]: 3.838 0.000 0.000 |a| = 3.838</p><p> CELL| Vector b [angstrom]: 1.919 3.323 0.000 |b| = 3.838</p><p> CELL| Vector c [angstrom]: 1.919 1.108 3.133 |c| = 3.838</p><span lang="EN"><p> CELL| Angle (b,c), alpha [degree]: 60.000</p><p> CELL| Angle (a,c), beta [degree]: 60.000</p><p> CELL| Angle (a,b), gamma [degree]: 60.000</p><p> CELL| Requested initial symmetry: RHOMBOHEDRAL</p><p> CELL| Numerically orthorhombic: NO</p></span><p> </p><p>And its final cell structure is</p></span><span lang="EN"><p>CELL| Volume [angstrom^3]: 137.274</p><p> CELL| Vector a [angstrom]: 5.790 0.000 0.000 |a| = 5.790</p><p> CELL| Vector b [angstrom]: 2.895 5.015 0.000 |b| = 5.790</p><p> CELL| Vector c [angstrom]: 2.895 1.672 4.728 |c| = 5.790</p><p> CELL| Angle (b,c), alpha [degree]: 60.000</p><p> CELL| Angle (a,c), beta [degree]: 60.000</p><p> CELL| Angle (a,b), gamma [degree]: 60.000</p><p> CELL| Requested initial symmetry: RHOMBOHEDRAL</p><p> CELL| Numerically orthorhombic: NO</p><p> </p><p>And the final geometry is</p><span lang="EN"><p> i = 45, E = -7.6936438860</p><p> Si 4.1049115417 -0.4237817114 4.7278581917</p><p> Si 0.0000000000 0.0000000000 0.0000000000</p><p>The Si-Si length is clearly too long.</p><p> </p><p> </p><p> </p><p> </p><p>For the Si8 case, things appear quite normal.</p><p>Input:</p><span lang="EN"><p>&GLOBAL</p><p>
</p><p> PROJECT Si_bulk8</p><p>
</p><p> RUN_TYPE CELL_OPT</p><p>
</p><p> PRINT_LEVEL MEDIUM</p><p>
</p><p>&END GLOBAL</p><p>
</p><p>&FORCE_EVAL</p><p>
</p><p> METHOD Quickstep</p><p>
</p><p> STRESS_TENSOR ANALYTICAL</p><p>
</p><p> &SUBSYS</p><p>
</p><p> &KIND Si</p><p>
</p><p> ELEMENT Si</p><p>
</p><p> BASIS_SET DZVP-GTH-PADE</p><p>
</p><p> POTENTIAL GTH-PADE-q4</p><p>
</p><p> &END KIND</p><p>
</p><p> &CELL</p><p>
</p><p> A 5.430697500 0.000000000 0.000000000</p><p>
</p><p> B 0.000000000 5.430697500 0.000000000</p><p>
</p><p> C 0.000000000 0.000000000 5.430697500</p><p>
</p><p> SYMMETRY CUBIC</p><p>
</p><p> PERIODIC XYZ</p><p>
</p><p> &END CELL</p><p>
</p><p> &COORD</p><p>
</p><p> Si 0.000000000 0.000000000 0.000000000</p><p>
</p><p> Si 0.000000000 2.715348700 2.715348700</p><p>
</p><p> Si 2.715348700 2.715348700 0.000000000</p><p>
</p><p> Si 2.715348700 0.000000000 2.715348700</p><p>
</p><p> Si 4.073023100 1.357674400 4.073023100</p><p>
</p><p> Si 1.357674400 1.357674400 1.357674400</p><p>
</p><p> Si 1.357674400 4.073023100 4.073023100</p><p>
</p><p> Si 4.073023100 4.073023100 1.357674400</p><p>
</p><p> &END COORD</p><p>
</p><p> &END SUBSYS</p><p>
</p><p> &DFT</p><p>
</p><p> BASIS_SET_FILE_NAME BASIS_SET</p><p>
</p><p> POTENTIAL_FILE_NAME GTH_POTENTIALS</p><p>
</p><p> &QS</p><p>
</p><p> EPS_DEFAULT 1.0E-10</p><p>
</p><p> &END QS</p><p>
</p><p> &MGRID</p><p>
</p><p> NGRIDS 4</p><p>
</p><p> CUTOFF 300</p><p>
</p><p> REL_CUTOFF 60</p><p>
</p><p> &END MGRID</p><p>
</p><p> &XC</p><p>
</p><p> &XC_FUNCTIONAL PADE</p><p>
</p><p> &END XC_FUNCTIONAL</p><p>
</p><p> &END XC</p><p>
</p><p> &SCF</p><p>
</p><p> SCF_GUESS ATOMIC</p><p>
</p><p> EPS_SCF 1.0E-7</p><p>
</p><p> MAX_SCF 300</p><p>
</p><p> ADDED_MOS 10</p><p>
</p><p> &DIAGONALIZATION ON</p><p>
</p><p> ALGORITHM STANDARD</p><p>
</p><p> &END DIAGONALIZATION</p><p>
</p><p> &MIXING T</p><p>
</p><p> METHOD BROYDEN_MIXING</p><p>
</p><p> ALPHA 0.4</p><p>
</p><p> NBROYDEN 8</p><p>
</p><p> &END MIXING</p><p>
</p><p> &SMEAR ON</p><p>
</p><p> METHOD FERMI_DIRAC</p><p>
</p><p> ELECTRONIC_TEMPERATURE [K] 300</p><p>
</p><p> &END SMEAR</p><p>
</p><p> &END SCF</p><p>
</p><p> &END DFT</p><p>
</p><p> &PRINT</p><p>
</p><p> &FORCES ON</p><p>
</p><p> &END FORCES</p><p>
</p><p> &END PRINT</p><p>
</p><p>&END FORCE_EVAL</p><p>
</p><p>&MOTION</p><p>
</p><p> &CELL_OPT</p><p>
</p><p> KEEP_ANGLES</p><p>
</p><p> KEEP_SYMMETRY</p><p>
</p><p> &END CELL_OPT</p><p>
</p><p> &GEO_OPT</p><p>
</p><p> TYPE MINIMIZATION</p><p>
</p><p> MAX_DR 1.0E-03</p><p>
</p><p> MAX_FORCE 1.0E-03</p><p>
</p><p> RMS_DR 1.0E-03 </p><p>
</p><p> RMS_FORCE 1.0E-03</p><p>
</p><p> MAX_ITER 200</p><p>
</p><p> OPTIMIZER BFGS</p><p>
</p><p> !&BFGS</p><p>
</p><p> ! MAX_STEEP_STEPS 0</p><p>
</p><p> ! RESTART_LIMIT 9.0E-01</p><p>
</p><p> !&END BFGS</p><p>
</p><p> &END GEO_OPT</p><p>
</p><p> &CONSTRAINT</p><p>
</p><p> &FIXED_ATOMS</p><p>
</p><p> COMPONENTS_TO_FIX XYZ</p><p>
</p><p> LIST 1</p><p>
</p><p> &END FIXED_ATOMS</p><p>
</p><p> &END CONSTRAINT</p><p>
</p><p>&END MOTION </p><p>
</p><p> </p><div>Final cell structure:</div><div><span lang="EN"><p> CELL| Volume [angstrom^3]: 173.162</p>
<p> CELL| Vector a [angstrom]: 5.574 0.000 0.000 |a| = 5.574</p>
<p> CELL| Vector b [angstrom]: 0.000 5.574 0.000 |b| = 5.574</p>
<p> CELL| Vector c [angstrom]: 0.000 0.000 5.574 |c| = 5.574</p>
<p> CELL| Angle (b,c), alpha [degree]: 90.000</p>
<p> CELL| Angle (a,c), beta [degree]: 90.000</p>
<p> CELL| Angle (a,b), gamma [degree]: 90.000</p>
<p> CELL| Requested initial symmetry: CUBIC</p>
<p> CELL| Numerically orthorhombic: YES</p></span></div></span><div> </div><div>Final geometry</div><div><span lang="EN"><p> i = 4, E = -31.3087094725</p>
<p> Si 0.0000000000 0.0000000000 0.0000000000</p>
<p> Si -0.0000000224 2.7868973667 2.7868973671</p>
<p> Si 2.7868973677 2.7868973683 -0.0000000226</p>
<p> Si 2.7868973673 -0.0000000224 2.7868973679</p>
<p> Si 4.1803460577 1.3934486673 4.1803460580</p>
<p> Si 1.3934486913 1.3934486907 1.3934486902</p>
<p> Si 1.3934486666 4.1803460575 4.1803460574</p>
<p> Si 4.1803460579 4.1803460580 1.3934486678</p><p> </p><p>Could anyone help me with this confusion? Thanks a lot!</p></span></div><p> </p></span><p> </p></span><p> </p><div>
</div><p> </p></span></div></blockquote></div>