Trouble with CELL_OPT with unit cells of different sizes

Du Zhang melchiz... at gmail.com
Sat Feb 7 21:50:22 UTC 2015
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Hi Zhendong,
 
Thanks for your suggestion! 
 
I tried without fixing the atom for Si2, and the geometry is 
 

i = 20, E = -7.6373030835

Si 2.7020961928 0.9317906628 1.3251881238

Si 0.0002037244 0.6283827813 -0.2219791667

And the cell structure given by

CELL| Volume [angstrom^3]: 111.629

CELL| Vector a [angstrom]: 5.405 0.000 0.000 |a| = 5.405

CELL| Vector b [angstrom]: 2.702 4.681 0.000 |b| = 5.405

CELL| Vector c [angstrom]: 2.702 1.560 4.413 |c| = 5.405

CELL| Angle (b,c), alpha [degree]: 60.000

CELL| Angle (a,c), beta [degree]: 60.000

CELL| Angle (a,b), gamma [degree]: 60.000

CELL| Requested initial symmetry: RHOMBOHEDRAL

CELL| Numerically orthorhombic: NO

It seems that the bond length is still far too long.

Any other thoughts on this from you all?

 

On Friday, February 6, 2015 at 11:14:44 AM UTC-4, Du Zhang wrote:

> Hi Everyone,
>  
> I ran into some confusing results when I attempted to perform the 
> following geometry optimizations on Si crystal with Si2 and Si8 unit cells. 
>  
> The input file for Si2:
>  
>
> &GLOBAL
>
> PROJECT Si_bulk2
>
> RUN_TYPE CELL_OPT
>
> PRINT_LEVEL MEDIUM
>
> &END GLOBAL
>
> &FORCE_EVAL
>
> METHOD Quickstep
>
> STRESS_TENSOR ANALYTICAL
>
> &SUBSYS
>
> &KIND Si
>
> ELEMENT Si
>
> BASIS_SET DZVP-GTH-PADE
>
> POTENTIAL GTH-PADE-q4
>
> &END KIND
>
> &CELL
>
> A 3.83753393 0.00000000 0.00000000
>
> B 1.91876697 3.32340187 0.00000000
>
> C 1.91876697 1.10780062 3.13333333
>
> SYMMETRY RHOMBOHEDRAL
>
> PERIODIC XYZ
>
> &END CELL
>
> &COORD
>
> Si 1.91876697 1.10780062 0.78333333
>
> Si 0.00000000 -0.00000000 -0.00000000
>
> &END COORD
>
> &END SUBSYS
>
> &DFT
>
> BASIS_SET_FILE_NAME BASIS_SET
>
> POTENTIAL_FILE_NAME GTH_POTENTIALS
>
> &QS
>
> EPS_DEFAULT 1.0E-10
>
> &END QS
>
> &MGRID
>
> NGRIDS 4
>
> CUTOFF 300
>
> REL_CUTOFF 60
>
> &END MGRID
>
> &XC
>
> &XC_FUNCTIONAL PADE
>
> &END XC_FUNCTIONAL
>
> &END XC
>
> &SCF
>
> SCF_GUESS ATOMIC
>
> EPS_SCF 1.0E-7
>
> MAX_SCF 300
>
> ADDED_MOS 10
>
> &DIAGONALIZATION ON
>
> ALGORITHM STANDARD
>
> &END DIAGONALIZATION
>
> &MIXING T
>
> METHOD BROYDEN_MIXING
>
> ALPHA 0.4
>
> NBROYDEN 8
>
> &END MIXING
>
> &SMEAR ON
>
> METHOD FERMI_DIRAC
>
> ELECTRONIC_TEMPERATURE [K] 300
>
> &END SMEAR
>
> &END SCF
>
> &END DFT
>
> &PRINT
>
> &FORCES ON
>
> &END FORCES
>
> &END PRINT
>
> &END FORCE_EVAL
>
> &MOTION
>
> &CELL_OPT
>
> KEEP_ANGLES
>
> KEEP_SYMMETRY
>
> &END CELL_OPT
>
> &GEO_OPT
>
> TYPE MINIMIZATION
>
> MAX_DR 1.0E-03
>
> MAX_FORCE 1.0E-03
>
> RMS_DR 1.0E-03 
>
> RMS_FORCE 1.0E-03
>
> MAX_ITER 200
>
> OPTIMIZER BFGS
>
> !&BFGS
>
> ! MAX_STEEP_STEPS 0
>
> ! RESTART_LIMIT 9.0E-01
>
> !&END BFGS
>
> &END GEO_OPT
>
> &CONSTRAINT
>
> &FIXED_ATOMS
>
> COMPONENTS_TO_FIX XYZ
>
> LIST 2
>
> &END FIXED_ATOMS
>
> &END CONSTRAINT
>
> &END MOTION 
>
> Its initial cell structure is given by:
>
> CELL| Volume [angstrom^3]: 39.961
>
> CELL| Vector a [angstrom]: 3.838 0.000 0.000 |a| = 3.838
>
> CELL| Vector b [angstrom]: 1.919 3.323 0.000 |b| = 3.838
>
> CELL| Vector c [angstrom]: 1.919 1.108 3.133 |c| = 3.838
>
> CELL| Angle (b,c), alpha [degree]: 60.000
>
> CELL| Angle (a,c), beta [degree]: 60.000
>
> CELL| Angle (a,b), gamma [degree]: 60.000
>
> CELL| Requested initial symmetry: RHOMBOHEDRAL
>
> CELL| Numerically orthorhombic: NO
>
>  
>
> And its final cell structure is
>
> CELL| Volume [angstrom^3]: 137.274
>
> CELL| Vector a [angstrom]: 5.790 0.000 0.000 |a| = 5.790
>
> CELL| Vector b [angstrom]: 2.895 5.015 0.000 |b| = 5.790
>
> CELL| Vector c [angstrom]: 2.895 1.672 4.728 |c| = 5.790
>
> CELL| Angle (b,c), alpha [degree]: 60.000
>
> CELL| Angle (a,c), beta [degree]: 60.000
>
> CELL| Angle (a,b), gamma [degree]: 60.000
>
> CELL| Requested initial symmetry: RHOMBOHEDRAL
>
> CELL| Numerically orthorhombic: NO
>
>  
>
> And the final geometry is
>
> i = 45, E = -7.6936438860
>
> Si 4.1049115417 -0.4237817114 4.7278581917
>
> Si 0.0000000000 0.0000000000 0.0000000000
>
> The Si-Si length is clearly too long.
>
>  
>
>  
>
>  
>
>  
>
> For the Si8 case, things appear quite normal.
>
> Input:
>
> &GLOBAL
>
>  PROJECT Si_bulk8
>
>  RUN_TYPE CELL_OPT
>
>  PRINT_LEVEL MEDIUM
>
> &END GLOBAL
>
> &FORCE_EVAL
>
>  METHOD Quickstep
>
>  STRESS_TENSOR ANALYTICAL
>
>  &SUBSYS
>
>  &KIND Si
>
>  ELEMENT Si
>
>  BASIS_SET DZVP-GTH-PADE
>
>  POTENTIAL GTH-PADE-q4
>
>  &END KIND
>
>  &CELL
>
>  A 5.430697500 0.000000000 0.000000000
>
>  B 0.000000000 5.430697500 0.000000000
>
>  C 0.000000000 0.000000000 5.430697500
>
>  SYMMETRY CUBIC
>
>  PERIODIC XYZ
>
>  &END CELL
>
>  &COORD
>
>  Si 0.000000000 0.000000000 0.000000000
>
>  Si 0.000000000 2.715348700 2.715348700
>
>  Si 2.715348700 2.715348700 0.000000000
>
>  Si 2.715348700 0.000000000 2.715348700
>
>  Si 4.073023100 1.357674400 4.073023100
>
>  Si 1.357674400 1.357674400 1.357674400
>
>  Si 1.357674400 4.073023100 4.073023100
>
>  Si 4.073023100 4.073023100 1.357674400
>
>  &END COORD
>
>  &END SUBSYS
>
>  &DFT
>
>  BASIS_SET_FILE_NAME BASIS_SET
>
>  POTENTIAL_FILE_NAME GTH_POTENTIALS
>
>  &QS
>
>  EPS_DEFAULT 1.0E-10
>
>  &END QS
>
>  &MGRID
>
>  NGRIDS 4
>
>  CUTOFF 300
>
>  REL_CUTOFF 60
>
>  &END MGRID
>
>  &XC
>
>  &XC_FUNCTIONAL PADE
>
>  &END XC_FUNCTIONAL
>
>  &END XC
>
>  &SCF
>
>  SCF_GUESS ATOMIC
>
>  EPS_SCF 1.0E-7
>
>  MAX_SCF 300
>
>  ADDED_MOS 10
>
>  &DIAGONALIZATION ON
>
>  ALGORITHM STANDARD
>
>  &END DIAGONALIZATION
>
>  &MIXING T
>
>  METHOD BROYDEN_MIXING
>
>  ALPHA 0.4
>
>  NBROYDEN 8
>
>  &END MIXING
>
>  &SMEAR ON
>
>  METHOD FERMI_DIRAC
>
>  ELECTRONIC_TEMPERATURE [K] 300
>
>  &END SMEAR
>
>  &END SCF
>
>  &END DFT
>
>  &PRINT
>
>  &FORCES ON
>
>  &END FORCES
>
>  &END PRINT
>
> &END FORCE_EVAL
>
> &MOTION
>
>  &CELL_OPT
>
>  KEEP_ANGLES
>
>  KEEP_SYMMETRY
>
>  &END CELL_OPT
>
>  &GEO_OPT
>
>  TYPE MINIMIZATION
>
>  MAX_DR 1.0E-03
>
>  MAX_FORCE 1.0E-03
>
>  RMS_DR 1.0E-03 
>
>  RMS_FORCE 1.0E-03
>
>  MAX_ITER 200
>
>  OPTIMIZER BFGS
>
>  !&BFGS
>
>  ! MAX_STEEP_STEPS 0
>
>  ! RESTART_LIMIT 9.0E-01
>
>  !&END BFGS
>
>  &END GEO_OPT
>
>  &CONSTRAINT
>
>  &FIXED_ATOMS
>
>  COMPONENTS_TO_FIX XYZ
>
>  LIST 1
>
>  &END FIXED_ATOMS
>
>  &END CONSTRAINT
>
> &END MOTION 
>
>  Final cell structure:
>
> CELL| Volume [angstrom^3]: 173.162
>
> CELL| Vector a [angstrom]: 5.574 0.000 0.000 |a| = 5.574
>
> CELL| Vector b [angstrom]: 0.000 5.574 0.000 |b| = 5.574
>
> CELL| Vector c [angstrom]: 0.000 0.000 5.574 |c| = 5.574
>
> CELL| Angle (b,c), alpha [degree]: 90.000
>
> CELL| Angle (a,c), beta [degree]: 90.000
>
> CELL| Angle (a,b), gamma [degree]: 90.000
>
> CELL| Requested initial symmetry: CUBIC
>
> CELL| Numerically orthorhombic: YES
>  
> Final geometry
>
> i = 4, E = -31.3087094725
>
> Si 0.0000000000 0.0000000000 0.0000000000
>
> Si -0.0000000224 2.7868973667 2.7868973671
>
> Si 2.7868973677 2.7868973683 -0.0000000226
>
> Si 2.7868973673 -0.0000000224 2.7868973679
>
> Si 4.1803460577 1.3934486673 4.1803460580
>
> Si 1.3934486913 1.3934486907 1.3934486902
>
> Si 1.3934486666 4.1803460575 4.1803460574
>
> Si 4.1803460579 4.1803460580 1.3934486678
>
>  
>
> Could anyone help me with this confusion? Thanks a lot!
>
>  
>
>  
>
>  
>
>
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