[QE-users] problems of calculation of vibration frequency using ph.x
兵临城下
vegalew at qq.com
Tue Jan 22 15:39:28 CET 2019
Dear all,
The reviewers asked me to do zero-point corrections (ZPE) for water adsorbed on Fe surface slab.
I tried to use ph.x to calculate vibration frequency of adsorbed H2O on the surface.
But when I finished the scf calculation, ph.x made the CPU cores rushing madly without output...
Then I simplified the system with one water molecule in the supercell of 12.5x12.5x21 Angstrom^3. The ph.x could calculate 9 vibration frequencies successfully. But it seems a little bit slow.
But when I simplified the system with 16 Fe atoms on first layer of surface slab in the supercell of 12.5x12.5x21 Angstrom^3 and removed the rest Fe atoms below the surface. The ph.x made the CPU cores mad again.
the input file for scf calculation of Fe atoms on first layer of surface slab as follows,
&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch' ,
outdir='/fs08/home/espresso-6.1/qe-6.1/tempdir/test-1.0.2x2/Fe' ,
prefix='test-1.0.2x2Fe',
pseudo_dir = '/fs08/home/qe-6.3/pseudo/' ,
etot_conv_thr = 4.0D-4 ,
forc_conv_thr = 4.0D-4 ,
tstress = .true. ,
tprnfor = .true. ,
wf_collect = .true. ,
/
&SYSTEM
ibrav = 0,
nosym = .true.,
A = 11.2840,
nat = 16,
ntyp = 1,
nspin = 2,
starting_magnetization(1)=0.6,
occupations='smearing',
smearing='mp',
degauss=0.05,
ecutwfc =64,
ecutrho =782.0
/
&ELECTRONS
mixing_mode ='local-TF',
mixing_beta=0.3,
/
CELL_PARAMETERS
1.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000
0.00000000 0.00000000 1.86569478
ATOMIC_SPECIES
Fe 55.85 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
ATOMIC_POSITIONS crystal
Fe -0.000070162 -0.001364954 0.336563416
Fe 0.249801425 -0.000872680 0.336864779
Fe 0.499934921 -0.002545661 0.336890374
Fe 0.750021168 -0.000874476 0.336865169
Fe -0.000045769 0.249376170 0.336866355
Fe 0.249625654 0.248725837 0.336534575
Fe 0.499939806 0.248410455 0.336312079
Fe 0.750318855 0.248696436 0.336528914
Fe -0.000005167 0.498750484 0.336896061
Fe 0.246009504 0.499503888 0.335983876
Fe 0.500263595 0.496421434 0.341364152
Fe 0.753992382 0.499521417 0.335970703
Fe -0.000037116 0.749380804 0.336858971
Fe 0.250321424 0.748218135 0.336582066
Fe 0.499946787 0.755247262 0.335688659
Fe 0.749616030 0.748261810 0.336570775
K_POINTS automatic
2 2 1 0 0 0
The input file for ph.x as follows,
test
&INPUTPH
outdir='/fs08/home/espresso-6.1/qe-6.1/tempdir/test-1.0.2x2/Fe' ,
prefix='test-1.0.2x2Fe',
fildyn='test.dynG',
nat_todo=1
/
0.0 0.0 0.0
1
The output of ph.x as follows,
Program PHONON v.6.3 starts on 22Jan2019 at 19:46:26
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);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 24 processors
MPI processes distributed on 1 nodes
R & G space division: proc/nbgrp/npool/nimage = 24
Reading data from directory:
/fs08/home/espresso-6.1/qe-6.1/tempdir/test-1.0.2x2/Fe/test-1.0.2x2Fe.save/
IMPORTANT: XC functional enforced from input :
Exchange-correlation = PBE ( 1 4 3 4 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
file Fe.pbe-spn-kjpaw_psl.0.2.1.UPF: wavefunction(s) 3D renormalized
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 1178 386 101 278340 52130 7032
Max 1179 387 103 278345 52141 7038
Sum 28293 9265 2441 6680231 1251139 168823
Generating pointlists ...
new r_m : 0.0999 (alat units) 2.1305 (a.u.) for type 1
Check: negative/imaginary core charge= -0.000004 0.000000
negative rho (up, down): 2.283E-04 2.603E-03
Calculation of q = 0.0000000 0.0000000 0.0000000
Possibly too few bands at point 1 0.00000 0.00000 0.00000
Possibly too few bands at point 2 0.00000 -0.50000 0.00000
Possibly too few bands at point 3 -0.50000 0.00000 0.00000
Possibly too few bands at point 4 -0.50000 -0.50000 0.00000
Possibly too few bands at point 5 0.00000 0.00000 0.00000
Possibly too few bands at point 6 0.00000 -0.50000 0.00000
Possibly too few bands at point 7 -0.50000 0.00000 0.00000
Possibly too few bands at point 8 -0.50000 -0.50000 0.00000
test
bravais-lattice index = 0
lattice parameter (alat) = 21.3237 a.u.
unit-cell volume = 18089.4947 (a.u.)^3
number of atoms/cell = 16
number of atomic types = 1
kinetic-energy cut-off = 64.0000 Ry
charge density cut-off = 782.0000 Ry
convergence threshold = 1.0E-12
beta = 0.7000
number of iterations used = 4
Exchange-correlation = PBE ( 1 4 3 4 0 0)
celldm(1)= 21.32367 celldm(2)= 0.00000 celldm(3)= 1.86569
celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.0000 0.0000 0.0000 )
a(2) = ( 0.0000 1.0000 0.0000 )
a(3) = ( 0.0000 0.0000 1.8657 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.0000 0.0000 0.0000 )
b(2) = ( 0.0000 1.0000 0.0000 )
b(3) = ( 0.0000 0.0000 0.5360 )
Atoms inside the unit cell:
Cartesian axes
site n. atom mass positions (alat units)
1 Fe 55.8500 tau( 1) = ( -0.00007 -0.00136 0.62792 )
2 Fe 55.8500 tau( 2) = ( 0.24980 -0.00087 0.62849 )
3 Fe 55.8500 tau( 3) = ( 0.49993 -0.00255 0.62853 )
4 Fe 55.8500 tau( 4) = ( 0.75002 -0.00087 0.62849 )
5 Fe 55.8500 tau( 5) = ( -0.00005 0.24938 0.62849 )
6 Fe 55.8500 tau( 6) = ( 0.24963 0.24873 0.62787 )
7 Fe 55.8500 tau( 7) = ( 0.49994 0.24841 0.62746 )
8 Fe 55.8500 tau( 8) = ( 0.75032 0.24870 0.62786 )
9 Fe 55.8500 tau( 9) = ( -0.00001 0.49875 0.62855 )
10 Fe 55.8500 tau( 10) = ( 0.24601 0.49950 0.62684 )
11 Fe 55.8500 tau( 11) = ( 0.50026 0.49642 0.63688 )
12 Fe 55.8500 tau( 12) = ( 0.75399 0.49952 0.62682 )
13 Fe 55.8500 tau( 13) = ( -0.00004 0.74938 0.62848 )
14 Fe 55.8500 tau( 14) = ( 0.25032 0.74822 0.62796 )
15 Fe 55.8500 tau( 15) = ( 0.49995 0.75525 0.62629 )
16 Fe 55.8500 tau( 16) = ( 0.74962 0.74826 0.62794 )
Computing dynamical matrix for
q = ( 0.0000000 0.0000000 0.0000000 )
2 Sym.Ops. (with q -> -q+G )
G cutoff = 9006.8081 ( 278343 G-vectors) FFT grid: (192,192,360)
G cutoff = 2948.5203 ( 52132 G-vectors) smooth grid: (120,120,216)
number of k points= 8 mp smearing, width (Ry)= 0.0500
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000
k( 2) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.2500000
k( 3) = ( -0.5000000 0.0000000 0.0000000), wk = 0.2500000
k( 4) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.2500000
k( 5) = ( 0.0000000 0.0000000 0.0000000), wk = 0.2500000
k( 6) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.2500000
k( 7) = ( -0.5000000 0.0000000 0.0000000), wk = 0.2500000
k( 8) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.2500000
PseudoPot. # 1 for Fe read from file:
/fs08/home/js_wjliu/qe-6.3/pseudo/Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
MD5 check sum: 4338034a7fd945be4bb7db5fd3b2d142
Pseudo is Projector augmented-wave + core cor, Zval = 16.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1191 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2
Q(r) pseudized with 0 coefficients
Mode symmetry, C_1 (1) point group:
Atomic displacements:
There are 48 irreducible representations
Representation 1 1 modes -A To be done
Representation 2 1 modes -A To be done
Representation 3 1 modes -A To be done
Representation 4 1 modes -A Not done in this run
Representation 5 1 modes -A Not done in this run
Representation 6 1 modes -A Not done in this run
Representation 7 1 modes -A Not done in this run
Representation 8 1 modes -A Not done in this run
Representation 9 1 modes -A Not done in this run
Representation 10 1 modes -A Not done in this run
Representation 11 1 modes -A Not done in this run
Representation 12 1 modes -A Not done in this run
Representation 13 1 modes -A Not done in this run
Representation 14 1 modes -A Not done in this run
Representation 15 1 modes -A Not done in this run
Representation 16 1 modes -A Not done in this run
Representation 17 1 modes -A Not done in this run
Representation 18 1 modes -A Not done in this run
Representation 19 1 modes -A Not done in this run
Representation 20 1 modes -A Not done in this run
Representation 21 1 modes -A Not done in this run
Representation 22 1 modes -A Not done in this run
Representation 23 1 modes -A Not done in this run
Representation 24 1 modes -A Not done in this run
Representation 25 1 modes -A Not done in this run
Representation 26 1 modes -A Not done in this run
Representation 27 1 modes -A Not done in this run
Representation 28 1 modes -A Not done in this run
Representation 29 1 modes -A Not done in this run
Representation 30 1 modes -A Not done in this run
Representation 31 1 modes -A Not done in this run
Representation 32 1 modes -A Not done in this run
Representation 33 1 modes -A Not done in this run
Representation 34 1 modes -A Not done in this run
Representation 35 1 modes -A Not done in this run
Representation 36 1 modes -A Not done in this run
Representation 37 1 modes -A Not done in this run
Representation 38 1 modes -A Not done in this run
Representation 39 1 modes -A Not done in this run
Representation 40 1 modes -A Not done in this run
Representation 41 1 modes -A Not done in this run
Representation 42 1 modes -A Not done in this run
Representation 43 1 modes -A Not done in this run
Representation 44 1 modes -A Not done in this run
Representation 45 1 modes -A Not done in this run
Representation 46 1 modes -A Not done in this run
Representation 47 1 modes -A Not done in this run
Representation 48 1 modes -A Not done in this run
Compute atoms: 1,
Then the CPU cores runs madly for days, but the output file never updates at all.
I have tested it with 6.1,6.2,6.3 versions of QE. The situation remains the same.
My QE is compiled by intel compilers. openmpi 1.10.0 is also used for parallel calculation.
Any help will be deeply appreciated.
best wishes
vega
------------------
------------------
vega
Department of physics, Nanjing University, China
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190122/894c8e7f/attachment.html>
More information about the users
mailing list