Dear all, I have a question regarding constructing supercells in QE and performing vc-relax. Based on recommendations available on pwscf website, I used xcrysden to generate a rather large cell (consisting 125 atoms of vanadium, available in attached file). But, when I modify my input script and again visualize the structure, "translational asymmetric cell" view shows a very strange configuration of atoms. Also, performing vc-relax takes incredibly long time (about 6 days on 64-cores). Is there something wrong with my method? Is this a correct super cell? I use QE5.4.0 compiled with ifort. --------------------------------------------------------------------------------------------------------------------- Method:
1- Constructing a simple bcc unit cell (~ in1.txt) 2- Visualizing using xcrysden, changing to primitive cell mode, repeating cell in x,y and z-direction (5x5x5) and saving configuration (~ data.xyz) 3- Extracting atomic positions from saved configuration and modifying the input script (in2.txt) Thank you very much for your response. -- With Best Regards Afshin Arjhangemehr PhD candidate in Radiation Application Shahid Beheshti University G.C, Tehran, IRAN (+98) 912 439 20 64
&CONTROL
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
etot_conv_thr = 1.0E-8 ,
forc_conv_thr = 1.0D-8 ,
outdir='/home/koma/software/QE-USER/Output',
pseudo_dir = '/home/koma/software/QE-USER/Pseudo-potential',
tprnfor = .true.
tstress = .true.
/
&SYSTEM
ibrav = 3,
celldm(1) = 5.62586,
nat = 1,
ntyp = 1,
ecutwfc = 100
occupations = 'smearing' ,
degauss= 0.01 ,
smearing= 'gaussian',
nspin=2 ,
starting_magnetization(1) = 0.2 ,
/
&ELECTRONS
conv_thr = 1.D-8 ,
/
&IONS
ion_dynamics= 'bfgs',
upscale = 70.d0,
pot_extrapolation = 'atomic',
wfc_extrapolation = 'none' ,
/
ATOMIC_SPECIES
V 50.6941 V.pbe-spn-kjpaw_psl.0.2.3.UPF
ATOMIC_POSITIONS (angstrom)
V 0 0 0
K_POINTS {automatic}
16 16 16 0 0 0
data.xyz
Description: Protein Databank data
&CONTROL
calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
prefix = 'V_125atoms' ,
etot_conv_thr = 1.0E-2 ,
forc_conv_thr = 1.0D-2 ,
outdir='/share/users/mahdiani/espresso/Output',
pseudo_dir = '/share/users/mahdiani/espresso/PS',
tprnfor = .true.
tstress = .true.
/
&SYSTEM
ibrav = 3,
celldm(1) = 28.6293 ,
nat = 125,
ntyp = 1,
ecutwfc = 47 ,
occupations = 'smearing' ,
degauss= 0.05 ,
smearing= 'gaussian',
nspin=2 ,
starting_magnetization(1) = 0.05 ,
/
&ELECTRONS
conv_thr = 1.D-2 ,
/
&IONS
ion_dynamics= 'bfgs',
upscale = 70.d0,
pot_extrapolation = 'atomic',
wfc_extrapolation = 'none' ,
/
&CELL
cell_dynamics = 'bfgs' ,
cell_factor = 2 ,
/
ATOMIC_SPECIES
V 50.6941 V.pbe-spn-kjpaw_psl.0.2.3.UPF
ATOMIC_POSITIONS (angstrom)
V 0.0000000000 0.0000000000 0.0000000000
V -1.5149967090 -1.5149967090 1.5149967090
V -3.0299934180 -3.0299934180 3.0299934180
V -4.5449901270 -4.5449901270 4.5449901270
V -6.0599868360 -6.0599868360 6.0599868360
V -1.5149967090 1.5149967090 1.5149967090
V -3.0299934180 0.0000000000 3.0299934180
V -4.5449901270 -1.5149967090 4.5449901270
V -6.0599868360 -3.0299934180 6.0599868360
V -7.5749835450 -4.5449901270 7.5749835450
V -3.0299934180 3.0299934180 3.0299934180
V -4.5449901270 1.5149967090 4.5449901270
V -6.0599868360 0.0000000000 6.0599868360
V -7.5749835450 -1.5149967090 7.5749835450
V -9.0899802540 -3.0299934180 9.0899802540
V -4.5449901270 4.5449901270 4.5449901270
V -6.0599868360 3.0299934180 6.0599868360
V -7.5749835450 1.5149967090 7.5749835450
V -9.0899802540 0.0000000000 9.0899802540
V -10.6049769630 -1.5149967090 10.6049769630
V -6.0599868360 6.0599868360 6.0599868360
V -7.5749835450 4.5449901270 7.5749835450
V -9.0899802540 3.0299934180 9.0899802540
V -10.6049769630 1.5149967090 10.6049769630
V -12.1199736720 0.0000000000 12.1199736720
V 1.5149967090 1.5149967090 1.5149967090
V 0.0000000000 0.0000000000 3.0299934180
V -1.5149967090 -1.5149967090 4.5449901270
V -3.0299934180 -3.0299934180 6.0599868360
V -4.5449901270 -4.5449901270 7.5749835450
V 0.0000000000 3.0299934180 3.0299934180
V -1.5149967090 1.5149967090 4.5449901270
V -3.0299934180 0.0000000000 6.0599868360
V -4.5449901270 -1.5149967090 7.5749835450
V -6.0599868360 -3.0299934180 9.0899802540
V -1.5149967090 4.5449901270 4.5449901270
V -3.0299934180 3.0299934180 6.0599868360
V -4.5449901270 1.5149967090 7.5749835450
V -6.0599868360 0.0000000000 9.0899802540
V -7.5749835450 -1.5149967090 10.6049769630
V -3.0299934180 6.0599868360 6.0599868360
V -4.5449901270 4.5449901270 7.5749835450
V -6.0599868360 3.0299934180 9.0899802540
V -7.5749835450 1.5149967090 10.6049769630
V -9.0899802540 0.0000000000 12.1199736720
V -4.5449901270 7.5749835450 7.5749835450
V -6.0599868360 6.0599868360 9.0899802540
V -7.5749835450 4.5449901270 10.6049769630
V -9.0899802540 3.0299934180 12.1199736720
V -10.6049769630 1.5149967090 13.6349703810
V 3.0299934180 3.0299934180 3.0299934180
V 1.5149967090 1.5149967090 4.5449901270
V 0.0000000000 0.0000000000 6.0599868360
V -1.5149967090 -1.5149967090 7.5749835450
V -3.0299934180 -3.0299934180 9.0899802540
V 1.5149967090 4.5449901270 4.5449901270
V 0.0000000000 3.0299934180 6.0599868360
V -1.5149967090 1.5149967090 7.5749835450
V -3.0299934180 0.0000000000 9.0899802540
V -4.5449901270 -1.5149967090 10.6049769630
V 0.0000000000 6.0599868360 6.0599868360
V -1.5149967090 4.5449901270 7.5749835450
V -3.0299934180 3.0299934180 9.0899802540
V -4.5449901270 1.5149967090 10.6049769630
V -6.0599868360 0.0000000000 12.1199736720
V -1.5149967090 7.5749835450 7.5749835450
V -3.0299934180 6.0599868360 9.0899802540
V -4.5449901270 4.5449901270 10.6049769630
V -6.0599868360 3.0299934180 12.1199736720
V -7.5749835450 1.5149967090 13.6349703810
V -3.0299934180 9.0899802540 9.0899802540
V -4.5449901270 7.5749835450 10.6049769630
V -6.0599868360 6.0599868360 12.1199736720
V -7.5749835450 4.5449901270 13.6349703810
V -9.0899802540 3.0299934180 15.1499670900
V 4.5449901270 4.5449901270 4.5449901270
V 3.0299934180 3.0299934180 6.0599868360
V 1.5149967090 1.5149967090 7.5749835450
V 0.0000000000 0.0000000000 9.0899802540
V -1.5149967090 -1.5149967090 10.6049769630
V 3.0299934180 6.0599868360 6.0599868360
V 1.5149967090 4.5449901270 7.5749835450
V 0.0000000000 3.0299934180 9.0899802540
V -1.5149967090 1.5149967090 10.6049769630
V -3.0299934180 0.0000000000 12.1199736720
V 1.5149967090 7.5749835450 7.5749835450
V 0.0000000000 6.0599868360 9.0899802540
V -1.5149967090 4.5449901270 10.6049769630
V -3.0299934180 3.0299934180 12.1199736720
V -4.5449901270 1.5149967090 13.6349703810
V 0.0000000000 9.0899802540 9.0899802540
V -1.5149967090 7.5749835450 10.6049769630
V -3.0299934180 6.0599868360 12.1199736720
V -4.5449901270 4.5449901270 13.6349703810
V -6.0599868360 3.0299934180 15.1499670900
V -1.5149967090 10.6049769630 10.6049769630
V -3.0299934180 9.0899802540 12.1199736720
V -4.5449901270 7.5749835450 13.6349703810
V -6.0599868360 6.0599868360 15.1499670900
V -7.5749835450 4.5449901270 16.6649637990
V 6.0599868360 6.0599868360 6.0599868360
V 4.5449901270 4.5449901270 7.5749835450
V 3.0299934180 3.0299934180 9.0899802540
V 1.5149967090 1.5149967090 10.6049769630
V 0.0000000000 0.0000000000 12.1199736720
V 4.5449901270 7.5749835450 7.5749835450
V 3.0299934180 6.0599868360 9.0899802540
V 1.5149967090 4.5449901270 10.6049769630
V 0.0000000000 3.0299934180 12.1199736720
V -1.5149967090 1.5149967090 13.6349703810
V 3.0299934180 9.0899802540 9.0899802540
V 1.5149967090 7.5749835450 10.6049769630
V 0.0000000000 6.0599868360 12.1199736720
V -1.5149967090 4.5449901270 13.6349703810
V -3.0299934180 3.0299934180 15.1499670900
V 1.5149967090 10.6049769630 10.6049769630
V 0.0000000000 9.0899802540 12.1199736720
V -1.5149967090 7.5749835450 13.6349703810
V -3.0299934180 6.0599868360 15.1499670900
V -4.5449901270 4.5449901270 16.6649637990
V 0.0000000000 12.1199736720 12.1199736720
V -1.5149967090 10.6049769630 13.6349703810
V -3.0299934180 9.0899802540 15.1499670900
V -4.5449901270 7.5749835450 16.6649637990
V -6.0599868360 6.0599868360 18.1799605080
K_POINTS {automatic}
2 2 2 0 0 0
_______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
