[Pw_forum] vc-relax of arsenate doped gypsum

Shaofeng Wang wangshaofeng at iae.ac.cn
Wed Dec 3 14:54:52 CET 2014


Dear QE users,

I am optimizing the geometry of arsenate doped gypsum. The primitive cell  
is used for calculation.
Firstly, I optimized the structure of gypsum using norm-conserving  
pseudopotential with ecutoff of 100ry. The input file is shown as follow:
  &CONTROL
                  calculation = 'vc-relax' ,
                       outdir =  
'/home/wangshaofeng/QEcalculation/1pcell/tmp' ,
                   pseudo_dir =  
'/home/wangshaofeng/QE/espresso-5.1.1/pseudo' ,
                       prefix = '1pcell_pbenc' ,
                etot_conv_thr = 1.0D-4 ,
                forc_conv_thr = 1.0D-3 ,
                      tstress = .true. ,
                      tprnfor = .true. ,
dt = 100,
  /
  &SYSTEM
                        ibrav = 14,
                    celldm(1) = 15.5218314188,
                    celldm(2) = 1,
                    celldm(3) = 0.690545180062821,
                    celldm(4) = -0.156089687246161,
                    celldm(5) = -0.156089687246161,
                    celldm(6) = -0.707970147153588,
                          nat = 24,
                         ntyp = 4,
                      ecutwfc = 100 ,
  /
  &ELECTRONS
             electron_maxstep = 100,
                     conv_thr = 1.0d-7 ,
                  mixing_beta = 0.7 ,
  /
  &IONS
                 ion_dynamics = 'bfgs' ,
  /
  &CELL
                 cell_dynamics = 'bfgs' ,
press = 0.d0 ,
  /
ATOMIC_SPECIES
     H    1  H.pbesol-n-nc.UPF
     O    1  O.pbesol-nc.UPF
     S   1  S.pbesol-n-nc.UPF
    Ca   1  Ca.pbesol-n-nc.UPF
ATOMIC_POSITIONS crystal
O        0.807062337   0.361222656   0.598570160
O        0.804053744   0.578534546   0.921161146
O        0.728847271   0.870006843   0.919139608
H        0.681045448   0.854822734   0.734900939
H        0.757937102   0.772987952   0.917355848
Ca       0.829881568   0.170116392   0.249999576
S        0.667927288   0.332072243   0.750000011
H        0.777283500   0.770707054   0.426944239
H        0.847172482   0.670300540   0.253676464
O        0.878026208   0.741858516   0.433856394
O        0.625158449   0.832930961   0.442306484
O        0.379011621   0.838616679   0.084585877
S       0.333597607   0.666403133   0.250000101
Ca       0.174983308   0.825016527   0.750000316
H        0.229292946   0.222715837   0.073055825
H        0.329700897   0.152828806   0.246325916
O        0.258140477   0.121974364   0.066141461
O        0.167068390   0.374841176   0.057693403
O        0.161383888   0.620989023   0.415414589
H        0.227011296   0.242062900   0.582643873
H        0.145176529   0.318954028   0.765098701
O        0.129993169   0.271151982   0.580859894
O        0.421467661   0.195947932   0.578839266
O        0.638776811   0.192937173   0.901429907
K_POINTS automatic
   3 3 3   0 0 0


I got the result of unit volume as follow
      unit-cell volume          =    1664.6918 (a.u.)^3
      new unit-cell volume =   1799.67107 a.u.^3 (   266.68374 Ang^3 )
      new unit-cell volume =   1770.78544 a.u.^3 (   262.40333 Ang^3 )
      new unit-cell volume =   1739.77917 a.u.^3 (   257.80867 Ang^3 )
      new unit-cell volume =   1749.14028 a.u.^3 (   259.19584 Ang^3 )
      new unit-cell volume =   1742.24598 a.u.^3 (   258.17421 Ang^3 )
      new unit-cell volume =   1733.38467 a.u.^3 (   256.86110 Ang^3 )
      new unit-cell volume =   1726.66969 a.u.^3 (   255.86605 Ang^3 )
      new unit-cell volume =   1714.44289 a.u.^3 (   254.05422 Ang^3 )
      new unit-cell volume =   1706.40106 a.u.^3 (   252.86255 Ang^3 )
      new unit-cell volume =   1703.61836 a.u.^3 (   252.45019 Ang^3 )
      new unit-cell volume =   1700.96607 a.u.^3 (   252.05716 Ang^3 )
      new unit-cell volume =   1697.52644 a.u.^3 (   251.54746 Ang^3 )
      new unit-cell volume =   1693.43205 a.u.^3 (   250.94074 Ang^3 )
      new unit-cell volume =   1690.09450 a.u.^3 (   250.44616 Ang^3 )
      new unit-cell volume =   1687.04705 a.u.^3 (   249.99458 Ang^3 )
      new unit-cell volume =   1685.18573 a.u.^3 (   249.71876 Ang^3 )
      new unit-cell volume =   1685.69034 a.u.^3 (   249.79353 Ang^3 )
      new unit-cell volume =   1687.08415 a.u.^3 (   250.00008 Ang^3 )
      new unit-cell volume =   1687.40033 a.u.^3 (   250.04693 Ang^3 )
      new unit-cell volume =   1686.23296 a.u.^3 (   249.87394 Ang^3 )
      new unit-cell volume =   1683.83191 a.u.^3 (   249.51814 Ang^3 )
      new unit-cell volume =   1681.92293 a.u.^3 (   249.23526 Ang^3 )
      new unit-cell volume =   1680.10228 a.u.^3 (   248.96547 Ang^3 )
      new unit-cell volume =   1677.66288 a.u.^3 (   248.60399 Ang^3 )
      new unit-cell volume =   1674.37345 a.u.^3 (   248.11654 Ang^3 )
      new unit-cell volume =   1673.79623 a.u.^3 (   248.03101 Ang^3 )
      new unit-cell volume =   1674.44298 a.u.^3 (   248.12685 Ang^3 )
      new unit-cell volume =   1676.55115 a.u.^3 (   248.43925 Ang^3 )
      new unit-cell volume =   1677.08832 a.u.^3 (   248.51885 Ang^3 )
      new unit-cell volume =   1676.48496 a.u.^3 (   248.42944 Ang^3 )
      new unit-cell volume =   1674.71104 a.u.^3 (   248.16657 Ang^3 )
      new unit-cell volume =   1671.50239 a.u.^3 (   247.69110 Ang^3 )
      new unit-cell volume =   1668.45081 a.u.^3 (   247.23890 Ang^3 )
      new unit-cell volume =   1667.77485 a.u.^3 (   247.13873 Ang^3 )
      new unit-cell volume =   1669.00148 a.u.^3 (   247.32050 Ang^3 )
      new unit-cell volume =   1670.64794 a.u.^3 (   247.56448 Ang^3 )
      new unit-cell volume =   1672.02362 a.u.^3 (   247.76833 Ang^3 )
      new unit-cell volume =   1672.62120 a.u.^3 (   247.85689 Ang^3 )
      new unit-cell volume =   1672.41622 a.u.^3 (   247.82651 Ang^3 )
      new unit-cell volume =   1671.30253 a.u.^3 (   247.66148 Ang^3 )
      new unit-cell volume =   1669.93158 a.u.^3 (   247.45833 Ang^3 )
      new unit-cell volume =   1669.06970 a.u.^3 (   247.33061 Ang^3 )
      new unit-cell volume =   1668.76527 a.u.^3 (   247.28550 Ang^3 )
      new unit-cell volume =   1668.68945 a.u.^3 (   247.27426 Ang^3 )
      new unit-cell volume =   1668.64904 a.u.^3 (   247.26827 Ang^3 )
      new unit-cell volume =   1668.61002 a.u.^3 (   247.26249 Ang^3 )
      new unit-cell volume =   1668.93783 a.u.^3 (   247.31107 Ang^3 )
      new unit-cell volume =   1669.48292 a.u.^3 (   247.39184 Ang^3 )
      new unit-cell volume =   1669.31259 a.u.^3 (   247.36660 Ang^3 )
      new unit-cell volume =   1669.12252 a.u.^3 (   247.33844 Ang^3 )
The final unit-cell volume is very close to the original cell volume.

Then I substituted one sulfur atom with arsenic atom and set tot_charge to  
be -1. The following is input file:

                  calculation = 'vc-relax' ,
                       outdir =  
'/home/wangshaofeng/QEcalculation/1pcell+as/tmp' ,
                   pseudo_dir =  
'/home/wangshaofeng/QE/espresso-5.1.1/pseudo' ,
                       prefix = '1pcell+as_pbenc' ,
                etot_conv_thr = 1.0D-4 ,
                forc_conv_thr = 1.0D-3 ,
                      tstress = .true. ,
                      tprnfor = .true. ,
dt = 100,
  /
  &SYSTEM
                        ibrav = 14,
                    celldm(1) = 15.5218314188,
                    celldm(2) = 1,
                    celldm(3) = 0.690545180062821,
                    celldm(4) = -0.156089687246161,
                    celldm(5) = -0.156089687246161,
                    celldm(6) = -0.707970147153588,
                          nat = 24,
                         ntyp = 5,
                      ecutwfc = 100 ,
                   tot_charge = -1.000000,
  /
  &ELECTRONS
             electron_maxstep = 100,
                     conv_thr = 1.0d-7 ,
                  mixing_beta = 0.7 ,
  /
  &IONS
                 ion_dynamics = 'bfgs' ,
  /
  &CELL
                 cell_dynamics = 'bfgs' ,
press = 0.d0 ,
  /
ATOMIC_SPECIES
     H    1  H.pbesol-n-nc.UPF
     O    1  O.pbesol-nc.UPF
     S   1  S.pbesol-n-nc.UPF
    Ca   1  Ca.pbesol-n-nc.UPF
    As   1  As.pbesol-n-nc.UPF
ATOMIC_POSITIONS crystal
O        0.807062337   0.361222656   0.598570160
O        0.804053744   0.578534546   0.921161146
O        0.728847271   0.870006843   0.919139608
H        0.681045448   0.854822734   0.734900939
H        0.757937102   0.772987952   0.917355848
Ca       0.829881568   0.170116392   0.249999576
As        0.667927288   0.332072243   0.750000011
H        0.777283500   0.770707054   0.426944239
H        0.847172482   0.670300540   0.253676464
O        0.878026208   0.741858516   0.433856394
O        0.625158449   0.832930961   0.442306484
O        0.379011621   0.838616679   0.084585877
S       0.333597607   0.666403133   0.250000101
Ca       0.174983308   0.825016527   0.750000316
H        0.229292946   0.222715837   0.073055825
H        0.329700897   0.152828806   0.246325916
O        0.258140477   0.121974364   0.066141461
O        0.167068390   0.374841176   0.057693403
O        0.161383888   0.620989023   0.415414589
H        0.227011296   0.242062900   0.582643873
H        0.145176529   0.318954028   0.765098701
O        0.129993169   0.271151982   0.580859894
O        0.421467661   0.195947932   0.578839266
O        0.638776811   0.192937173   0.901429907
K_POINTS automatic
   3 3 3   0 0 0


Finally, I got the cell volume change as follow:
      unit-cell volume          =    1664.6918 (a.u.)^3
      new unit-cell volume =   1821.76207 a.u.^3 (   269.95728 Ang^3 )
      new unit-cell volume =   1853.96860 a.u.^3 (   274.72980 Ang^3 )
      new unit-cell volume =   1887.33947 a.u.^3 (   279.67485 Ang^3 )
      new unit-cell volume =   1895.22611 a.u.^3 (   280.84353 Ang^3 )
      new unit-cell volume =   1894.99460 a.u.^3 (   280.80922 Ang^3 )
      new unit-cell volume =   1893.89685 a.u.^3 (   280.64655 Ang^3 )
      new unit-cell volume =   1889.81038 a.u.^3 (   280.04100 Ang^3 )
      new unit-cell volume =   1883.84213 a.u.^3 (   279.15660 Ang^3 )
      new unit-cell volume =   1877.32433 a.u.^3 (   278.19076 Ang^3 )
      new unit-cell volume =   1872.32304 a.u.^3 (   277.44965 Ang^3 )
      new unit-cell volume =   1871.20235 a.u.^3 (   277.28358 Ang^3 )
      new unit-cell volume =   1870.66273 a.u.^3 (   277.20361 Ang^3 )
      new unit-cell volume =   1869.97279 a.u.^3 (   277.10137 Ang^3 )
      new unit-cell volume =   1868.25680 a.u.^3 (   276.84709 Ang^3 )
      new unit-cell volume =   1866.58128 a.u.^3 (   276.59880 Ang^3 )
      new unit-cell volume =   1865.72849 a.u.^3 (   276.47243 Ang^3 )
      new unit-cell volume =   1866.02079 a.u.^3 (   276.51575 Ang^3 )
      new unit-cell volume =   1866.99775 a.u.^3 (   276.66052 Ang^3 )
      new unit-cell volume =   1867.40877 a.u.^3 (   276.72143 Ang^3 )
      new unit-cell volume =   1866.99998 a.u.^3 (   276.66085 Ang^3 )
      new unit-cell volume =   1865.76186 a.u.^3 (   276.47738 Ang^3 )
      new unit-cell volume =   1864.41566 a.u.^3 (   276.27789 Ang^3 )
      new unit-cell volume =   1863.23971 a.u.^3 (   276.10363 Ang^3 )
      new unit-cell volume =   1863.12508 a.u.^3 (   276.08665 Ang^3 )
      new unit-cell volume =   1863.43918 a.u.^3 (   276.13319 Ang^3 )
      new unit-cell volume =   1863.82310 a.u.^3 (   276.19008 Ang^3 )
      new unit-cell volume =   1864.01082 a.u.^3 (   276.21790 Ang^3 )
      new unit-cell volume =   1864.01082 a.u.^3 (   276.21790 Ang^3 )
      unit-cell volume          =    1864.0108 (a.u.)^3
It can be seen that the unit-cell volume increased from 1664.6918 (a.u.)^3  
to 1864.0108 (a.u.)^3 by around 12 %.
Are these results reasonable? Any comments?

Regards,

Shaofeng Wang, Ph.D

Institute of Applied Ecology, CAS, China




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