[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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