[Pw_forum] Phonon density of state calculation
farid taherkhani
faridtaherkhani at gmail.com
Tue Nov 5 15:58:28 CET 2013
Dear All ,
I going to calculate phonon density of state for Ir metal nanocluster. As
a first step I did scf calculation with the following input
&control
calculation='scf'
restart_mode='from_scratch',
pseudo_dir='directory where pseudopotentials are stored/',
outdir='directory where large files are written/'
prefix='PH',
pseudo_dir ='/home/farid/QE-5/espresso-5.0/pseudo',
outdir='/home/farid/Pictures/tmp',
/
&system
ibrav= 0, celldm(1)=7.2560000 nat= 55, ntyp= 1,
ecutwfc = 25, ecutrho = 250, occupations='smearing',
smearing='marzari-vanderbilt', degauss=0.01,
nspin=1, starting_magnetization=0, report=1
/
&electrons
conv_thr = 1.0d-8
mixing_beta = 0.2
/
CELL_PARAMETERS
4.00000000 -1.00000000 2.00000000
-4.00000000 3.0000000 2.00000000
1.00000000 3.00000000 -2.0000000
ATOMIC_SPECIES
Ir 192.22 Ir.pbe-n-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
Ir -4.5482075278 -0.3525234593 2.9167230638
Ir 1.6168474710 0.5841502804 -4.9420796919
Ir 4.0159189649 -2.8003334615 0.1289518487
Ir 2.1724160762 -1.4470962187 4.7623488301
Ir 0.8186910951 -3.3608476210 3.3422847708
Ir -2.2257297976 0.7825950113 3.6854167253
Ir 1.5145104208 -1.0433245729 2.2781364349
Ir -1.8840549279 -2.4444019393 -2.8579640302
Ir -2.5995487374 -0.1601366415 -3.9469145514
Ir -0.9795523784 -3.7679215373 1.4158635842
Ir -4.1328963876 -1.3162608920 -2.0398764140
Ir 0.3844938066 0.3996192473 4.3414286249
Ir 4.5636615211 1.8774306547 1.7921218716
Ir 2.3187254912 -1.7191181065 -3.9459412684
Ir -3.0416987476 -1.5095074240 4.5864890704
Ir -0.4003587255 3.2213427187 -1.8404124273
Ir -0.3133219656 -3.6517886203 -1.0848668282
Ir 4.1298009496 -1.3476959017 -2.0895910201
Ir -4.8411600705 -1.4284391096 0.5105004535
Ir -1.6696951266 -3.6875991791 3.9970382146
Ir 4.1385647968 2.3660136781 -2.8034997400
Ir -1.0126754950 -1.4224601504 2.9827751112
Ir 0.2917729408 3.2119996120 0.6833742414
Ir -3.2522522402 -2.6665844912 2.2105783285
Ir -0.3257157031 -1.4103235104 0.3874292516
Ir 0.4040625442 -1.2448534415 -2.1636396211
Ir -1.5847298696 2.9842796275 2.5229512545
Ir -0.4001083436 1.1362892709 -3.4157328771
Ir -2.6145282484 -0.3081256838 1.1310864246
Ir -2.6353637902 -2.5705311527 -0.3217739846
Ir -3.8654573782 1.8469514246 1.8554923917
Ir 1.5670295933 -3.3339618920 0.8315334703
Ir 2.9264610114 0.7456252827 3.6060829100
Ir 4.6686696348 3.3079370814 -0.3951406514
Ir 2.3600168209 0.5652699932 -2.4238841555
Ir 2.7964432403 3.7841483475 1.3873952754
Ir 2.1824554618 1.3290380829 1.1396249881
Ir 2.2411093278 -0.9626476685 -0.2575536371
Ir 2.2447464572 -3.2000361959 -1.7434100935
Ir -2.6471798898 2.0374106158 -2.4261015206
Ir -2.0679510956 2.2976083757 0.0651257099
Ir 0.3988514431 -3.4118255295 -3.5918675426
Ir -0.2436328937 -1.9814342600 5.3556083289
Ir 1.0530507517 2.7049206195 3.1231513842
Ir 4.0707183860 -0.6260260654 1.6504830420
Ir 4.1256933553 0.2032606619 -4.1928807178
Ir -0.3339456914 0.8308427340 1.8533889891
Ir 3.3047248467 -2.8393093690 2.7197357867
Ir 4.2542967469 0.8053244874 -0.5776302766
Ir -4.1894932815 0.8862555860 -0.6031549687
Ir 1.5901923373 2.7686888519 -3.5021323513
Ir -1.9264406471 -0.1907049581 -1.3973385717
Ir -0.3211804983 -1.1284273675 -4.6891035172
Ir 0.3601978846 0.9538590134 -0.7687717170
Ir 2.2414644048 3.0080179554 -1.0340441436
K_POINTS
10
0.1250000 0.1250000 0.1250000 1.00
0.1250000 0.1250000 0.3750000 3.00
0.1250000 0.1250000 0.6250000 3.00
0.1250000 0.1250000 0.8750000 3.00
0.1250000 0.3750000 0.3750000 3.00
0.1250000 0.3750000 0.6250000 6.00
0.1250000 0.3750000 0.8750000 6.00
0.1250000 0.6250000 0.6250000 3.00
0.3750000 0.3750000 0.3750000 1.00
0.3750000 0.3750000 0.6250000 3.00
After that I did phonon calculation with following input file
phonons of Ir
restart_mode='restart',
&inputph
tr2_ph=1.0d-14,
ldisp=.true.,
nq1=4, nq2=4, nq3=4
amass(1)=192.217,
prefix='PH',
outdir='/home/farid/Pictures/tmp',
fildyn='Ir.dyn',
/
then I get following output
Program PHONON v.5.0 starts on 5Nov2013 at 12: 7: 3
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details
at
http://www.quantum-espresso.org/quote.php
Parallel version (MPI), running on 14 processors
R & G space division: proc/pool = 14
Ultrasoft (Vanderbilt) Pseudopotentials
Info: using nr1, nr2, nr3 values from input
Info: using nr1s, nr2s, nr3s values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0)
EXX-fraction = 0.00
Any further DFT definition will be discarded
Please, verify this is what you really want
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 1466 586 199 131148 33144 6583
Max 1467 587 200 131149 33214 6586
Sum 20535 8213 2795 1836077 464515 92183
Check: negative/imaginary core charge= -0.000019 0.000000
negative rho (up, down): 0.305E-04 0.000E+00
Dynamical matrices for ( 4, 4, 4,) uniform grid of q-points
( 36q-points):
N xq(1) xq(2) xq(3)
1 0.000000000 0.000000000 0.000000000
2 0.027777778 0.055555556 -0.027777778
3 -0.055555556 -0.111111111 0.055555556
4 -0.013888889 0.034722222 0.045138889
5 0.013888889 0.090277778 0.017361111
6 -0.069444444 -0.076388889 0.100694444
7 -0.041666667 -0.020833333 0.072916667
8 0.027777778 -0.069444444 -0.090277778
9 0.055555556 -0.013888889 -0.118055556
10 -0.027777778 -0.180555556 -0.034722222
11 0.041666667 0.020833333 0.052083333
12 0.069444444 0.076388889 0.024305556
13 -0.013888889 -0.090277778 0.107638889
14 0.013888889 -0.034722222 0.079861111
15 0.027777778 0.055555556 0.097222222
16 0.055555556 0.111111111 0.069444444
17 -0.027777778 -0.055555556 0.152777778
18 0.000000000 0.000000000 0.125000000
19 0.069444444 -0.048611111 -0.038194444
20 0.097222222 0.006944444 -0.065972222
21 0.013888889 -0.159722222 0.017361111
22 0.041666667 -0.104166667 -0.010416667
23 0.055555556 -0.013888889 0.006944444
24 0.083333333 0.041666667 -0.020833333
25 0.000000000 -0.125000000 0.062500000
26 0.027777778 -0.069444444 0.034722222
27 -0.083333333 -0.041666667 -0.104166667
28 -0.055555556 0.013888889 -0.131944444
29 -0.138888889 -0.152777778 -0.048611111
30 -0.097222222 -0.006944444 -0.059027778
31 -0.069444444 0.048611111 -0.086805556
32 -0.152777778 -0.118055556 -0.003472222
33 -0.125000000 -0.062500000 -0.031250000
34 -0.055555556 -0.111111111 -0.194444444
35 -0.027777778 -0.055555556 -0.222222222
36 -0.111111111 -0.222222222 -0.138888889
Calculation of q = 0.0000000 0.0000000 0.0000000
bravais-lattice index = 0
lattice parameter (alat) = 7.2560 a.u.
unit-cell volume = 27505.8024 (a.u.)^3
number of atoms/cell = 55
number of atomic types = 1
kinetic-energy cut-off = 25.0000 Ry
charge density cut-off = 250.0000 Ry
convergence threshold = 1.0E-14
beta = 0.7000
number of iterations used = 4
Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0)
EXX-fraction = 0.00
celldm(1)= 7.25600 celldm(2)= 0.00000 celldm(3)= 0.00000
celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 4.0000 -1.0000 2.0000 )
a(2) = ( -4.0000 3.0000 2.0000 )
a(3) = ( 1.0000 3.0000 -2.0000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 0.1667 0.0833 0.2083 )
b(2) = ( -0.0556 0.1389 0.1806 )
b(3) = ( 0.1111 0.2222 -0.1111 )
Atoms inside the unit cell:
Cartesian axes
site n. atom mass positions (alat units)
1 Ir 192.2170 tau( 1) = ( -1.18452 -0.09181
0.75962 )
2 Ir 192.2170 tau( 2) = ( 0.42109 0.15213
-1.28710 )
3 Ir 192.2170 tau( 3) = ( 1.04589 -0.72931
0.03358 )
4 Ir 192.2170 tau( 4) = ( 0.56578 -0.37688
1.24029 )
5 Ir 192.2170 tau( 5) = ( 0.21322 -0.87529
0.87045 )
6 Ir 192.2170 tau( 6) = ( -0.57966 0.20382
0.95982 )
7 Ir 192.2170 tau( 7) = ( 0.39443 -0.27172
0.59331 )
8 Ir 192.2170 tau( 8) = ( -0.49068 -0.63661
-0.74432 )
9 Ir 192.2170 tau( 9) = ( -0.67702 -0.04171
-1.02792 )
10 Ir 192.2170 tau(10) = ( -0.25511 -0.98130
0.36874 )
11 Ir 192.2170 tau(11) = ( -1.07636 -0.34280
-0.53126 )
12 Ir 192.2170 tau(12) = ( 0.10014 0.10408
1.13067 )
13 Ir 192.2170 tau(13) = ( 1.18854 0.48895
0.46673 )
14 Ir 192.2170 tau(14) = ( 0.60388 -0.44772
-1.02767 )
15 Ir 192.2170 tau(15) = ( -0.79217 -0.39313
1.19449 )
16 Ir 192.2170 tau(16) = ( -0.10427 0.83895
-0.47931 )
17 Ir 192.2170 tau(17) = ( -0.08160 -0.95106
-0.28254 )
18 Ir 192.2170 tau(18) = ( 1.07555 -0.35099
-0.54421 )
19 Ir 192.2170 tau(19) = ( -1.26081 -0.37202
0.13295 )
20 Ir 192.2170 tau(20) = ( -0.43485 -0.96038
1.04097 )
21 Ir 192.2170 tau(21) = ( 1.07783 0.61620
-0.73013 )
22 Ir 192.2170 tau(22) = ( -0.26374 -0.37046
0.77682 )
23 Ir 192.2170 tau(23) = ( 0.07599 0.83652
0.17798 )
24 Ir 192.2170 tau(24) = ( -0.84700 -0.69448
0.57571 )
25 Ir 192.2170 tau(25) = ( -0.08483 -0.36730
0.10090 )
26 Ir 192.2170 tau(26) = ( 0.10523 -0.32421
-0.56349 )
27 Ir 192.2170 tau(27) = ( -0.41272 0.77721
0.65707 )
28 Ir 192.2170 tau(28) = ( -0.10420 0.29593
-0.88958 )
29 Ir 192.2170 tau(29) = ( -0.68092 -0.08025
0.29458 )
30 Ir 192.2170 tau(30) = ( -0.68634 -0.66946
-0.08380 )
31 Ir 192.2170 tau(31) = ( -1.00671 0.48101
0.48324 )
32 Ir 192.2170 tau(32) = ( 0.40811 -0.86828
0.21656 )
33 Ir 192.2170 tau(33) = ( 0.76216 0.19419
0.93916 )
34 Ir 192.2170 tau(34) = ( 1.21589 0.86151
-0.10291 )
35 Ir 192.2170 tau(35) = ( 0.61463 0.14722
-0.63127 )
36 Ir 192.2170 tau(36) = ( 0.72830 0.98553
0.36133 )
37 Ir 192.2170 tau(37) = ( 0.56839 0.34613
0.29680 )
38 Ir 192.2170 tau(38) = ( 0.58367 -0.25071
-0.06708 )
39 Ir 192.2170 tau(39) = ( 0.58461 -0.83341
-0.45405 )
40 Ir 192.2170 tau(40) = ( -0.68942 0.53062
-0.63185 )
41 Ir 192.2170 tau(41) = ( -0.53857 0.59838
0.01696 )
42 Ir 192.2170 tau(42) = ( 0.10388 -0.88856
-0.93545 )
43 Ir 192.2170 tau(43) = ( -0.06345 -0.51604
1.39480 )
44 Ir 192.2170 tau(44) = ( 0.27425 0.70446
0.81338 )
45 Ir 192.2170 tau(45) = ( 1.06016 -0.16304
0.42985 )
46 Ir 192.2170 tau(46) = ( 1.07448 0.05294
-1.09198 )
47 Ir 192.2170 tau(47) = ( -0.08697 0.21638
0.48269 )
48 Ir 192.2170 tau(48) = ( 0.86067 -0.73946
0.70832 )
49 Ir 192.2170 tau(49) = ( 1.10797 0.20974
-0.15044 )
50 Ir 192.2170 tau(50) = ( -1.09110 0.23081
-0.15708 )
51 Ir 192.2170 tau(51) = ( 0.41414 0.72107
-0.91208 )
52 Ir 192.2170 tau(52) = ( -0.50172 -0.04967
-0.36392 )
53 Ir 192.2170 tau(53) = ( -0.08365 -0.29388
-1.22121 )
54 Ir 192.2170 tau(54) = ( 0.09381 0.24842
-0.20022 )
55 Ir 192.2170 tau(55) = ( 0.58376 0.78340
-0.26930 )
Computing dynamical matrix for
q = ( 0.0000000 0.0000000 0.0000000 )
2 Sym.Ops. (with q -> -q+G )
G cutoff = 333.4071 ( 131149 G-vectors) FFT grid: (180,200,144)
G cutoff = 133.3628 ( 33159 G-vectors) smooth grid: (108,125, 90)
number of k points= 10 Marzari-Vanderbilt smearing, width (Ry)=
0.0100
PseudoPot. # 1 for Ir read from file:
/home/farid/QE-5/espresso-5.0/pseudo/Ir.pbe-n-rrkjus.UPF
MD5 check sum: 03a0ee1dfff440a89eccce3a606b7527
Pseudo is Ultrasoft + core correction, Zval = 9.0
Generated by new atomic code, or converted to UPF format
Using radial grid of 1277 points, 3 beta functions with:
l(1) = 2
l(2) = 2
l(3) = 1
Q(r) pseudized with 0 coefficients
Atomic displacements:
There are 165 irreducible representations
Representation 1 1 modes - To be done
Representation 2 1 modes - To be done
Representation 3 1 modes - To be done
Representation 4 1 modes - To be done
Representation 5 1 modes - To be done
Representation 6 1 modes - To be done
Representation 7 1 modes - To be done
Representation 8 1 modes - To be done
Representation 9 1 modes - To be done
Representation 10 1 modes - To be done
Representation 11 1 modes - To be done
Representation 12 1 modes - To be done
Representation 13 1 modes - To be done
Representation 14 1 modes - To be done
Representation 15 1 modes - To be done
Representation 16 1 modes - To be done
Representation 17 1 modes - To be done
Representation 18 1 modes - To be done
Representation 19 1 modes - To be done
Representation 20 1 modes - To be done
Representation 21 1 modes - To be done
Representation 22 1 modes - To be done
Representation 23 1 modes - To be done
Representation 24 1 modes - To be done
Representation 25 1 modes - To be done
Representation 26 1 modes - To be done
Representation 27 1 modes - To be done
Representation 28 1 modes - To be done
Representation 29 1 modes - To be done
Representation 30 1 modes - To be done
Representation 31 1 modes - To be done
Representation 32 1 modes - To be done
Representation 33 1 modes - To be done
Representation 34 1 modes - To be done
Representation 35 1 modes - To be done
Representation 36 1 modes - To be done
Representation 37 1 modes - To be done
Representation 38 1 modes - To be done
Representation 39 1 modes - To be done
Representation 40 1 modes - To be done
Representation 41 1 modes - To be done
Representation 42 1 modes - To be done
Representation 43 1 modes - To be done
Representation 44 1 modes - To be done
Representation 45 1 modes - To be done
Representation 46 1 modes - To be done
Representation 47 1 modes - To be done
Representation 48 1 modes - To be done
Representation 49 1 modes - To be done
Representation 50 1 modes - To be done
Representation 51 1 modes - To be done
Representation 52 1 modes - To be done
Representation 53 1 modes - To be done
Representation 54 1 modes - To be done
Representation 55 1 modes - To be done
Representation 56 1 modes - To be done
Representation 57 1 modes - To be done
Representation 58 1 modes - To be done
Representation 59 1 modes - To be done
Representation 60 1 modes - To be done
Representation 61 1 modes - To be done
Representation 62 1 modes - To be done
Representation 63 1 modes - To be done
Representation 64 1 modes - To be done
Representation 65 1 modes - To be done
Representation 66 1 modes - To be done
Representation 67 1 modes - To be done
Representation 68 1 modes - To be done
Representation 69 1 modes - To be done
Representation 70 1 modes - To be done
Representation 71 1 modes - To be done
Representation 72 1 modes - To be done
Representation 73 1 modes - To be done
Representation 74 1 modes - To be done
Representation 75 1 modes - To be done
Representation 76 1 modes - To be done
Representation 77 1 modes - To be done
Representation 78 1 modes - To be done
Representation 79 1 modes - To be done
Representation 80 1 modes - To be done
Representation 81 1 modes - To be done
Representation 82 1 modes - To be done
Representation 83 1 modes - To be done
Representation 84 1 modes - To be done
Representation 85 1 modes - To be done
Representation 86 1 modes - To be done
Representation 87 1 modes - To be done
Representation 88 1 modes - To be done
Representation 89 1 modes - To be done
Representation 90 1 modes - To be done
Representation 91 1 modes - To be done
Representation 92 1 modes - To be done
Representation 93 1 modes - To be done
Representation 94 1 modes - To be done
Representation 95 1 modes - To be done
Representation 96 1 modes - To be done
Representation 97 1 modes - To be done
Representation 98 1 modes - To be done
Representation 99 1 modes - To be done
Representation 100 1 modes - To be done
Representation 101 1 modes - To be done
Representation 102 1 modes - To be done
Representation 103 1 modes - To be done
Representation 104 1 modes - To be done
Representation 105 1 modes - To be done
Representation 106 1 modes - To be done
Representation 107 1 modes - To be done
Representation 108 1 modes - To be done
Representation 109 1 modes - To be done
Representation 110 1 modes - To be done
Representation 111 1 modes - To be done
Representation 112 1 modes - To be done
Representation 113 1 modes - To be done
Representation 114 1 modes - To be done
Representation 115 1 modes - To be done
Representation 116 1 modes - To be done
Representation 117 1 modes - To be done
Representation 118 1 modes - To be done
Representation 119 1 modes - To be done
Representation 120 1 modes - To be done
Representation 121 1 modes - To be done
Representation 122 1 modes - To be done
Representation 123 1 modes - To be done
Representation 124 1 modes - To be done
Representation 125 1 modes - To be done
Representation 126 1 modes - To be done
Representation 127 1 modes - To be done
Representation 128 1 modes - To be done
Representation 129 1 modes - To be done
Representation 130 1 modes - To be done
Representation 131 1 modes - To be done
Representation 132 1 modes - To be done
Representation 133 1 modes - To be done
Representation 134 1 modes - To be done
Representation 135 1 modes - To be done
Representation 136 1 modes - To be done
Representation 137 1 modes - To be done
Representation 138 1 modes - To be done
Representation 139 1 modes - To be done
Representation 140 1 modes - To be done
Representation 141 1 modes - To be done
Representation 142 1 modes - To be done
Representation 143 1 modes - To be done
Representation 144 1 modes - To be done
Representation 145 1 modes - To be done
Representation 146 1 modes - To be done
Representation 147 1 modes - To be done
Representation 148 1 modes - To be done
Representation 149 1 modes - To be done
Representation 150 1 modes - To be done
Representation 151 1 modes - To be done
Representation 152 1 modes - To be done
Representation 153 1 modes - To be done
Representation 154 1 modes - To be done
Representation 155 1 modes - To be done
Representation 156 1 modes - To be done
Representation 157 1 modes - To be done
Representation 158 1 modes - To be done
Representation 159 1 modes - To be done
Representation 160 1 modes - To be done
Representation 161 1 modes - To be done
Representation 162 1 modes - To be done
Representation 163 1 modes - To be done
Representation 164 1 modes - To be done
Representation 165 1 modes - To be done
As a result, computation of phonon was not perfect and job was not done.
Any help will be appreciated.
All the best,
Farid
--
Dr. Farid Taherkhani
Assistant Professor
Department of Chemistry
Razi University
Kermanshah, Iran
Tel: +98-831-4274569
Email: f.taherkhani at razi.ac.ir
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