[QE-users] What's the correct way to perform BOMD at a given temperature
Jibiao Li
jibiaoli at foxmail.com
Sat Jul 6 11:08:28 CEST 2019
Hi all,
I am working on surface diffusion of a single water molecule on Pd(111) at a given temperature (50K) by using molecular dynamics in pw.x. However, the output file shows that the system temperature continuously goes down. I am not sure whether I used correct parameters in the input to fix the target temperature. Is something wrong with my input file? What's the correct way to simulate the surface diffusion at a given temperature?
> grep 'temperature' bomd.pw.out
Starting temperature = 50.00 K
temperature is controlled by velocity rescaling (rescaling)
temperature = 50.00000000 K
temperature = 49.08451411 K
temperature = 47.34902025 K
temperature = 48.69776388 K
temperature = 48.67531303 K
temperature = 48.13806887 K
temperature = 47.77128183 K
temperature = 48.84955608 K
temperature = 49.99377244 K
temperature = 49.46353472 K
temperature = 48.20956748 K
temperature = 48.50820119 K
temperature = 48.74058134 K
temperature = 48.08050314 K
temperature = 46.19882695 K
temperature = 45.34486798 K
temperature = 46.04136511 K
temperature = 46.51546894 K
temperature = 45.64423710 K
temperature = 44.80023560 K
INPUT FILE
&CONTROL
calculation = 'md' ,
restart_mode = 'from_scratch' ,
outdir = './' ,
pseudo_dir = '/home/jibiaoli/pseudo/' ,
prefix = 'bomd' ,
nstep = 200 ,
tstress = .true. ,
tprnfor = .true. ,
dt = 50 ,
/
&SYSTEM
ibrav = 8,
celldm(1) = 15.596671813,
celldm(2) = 1.154699881261,
celldm(3) = 2.876257,
nat = 51,
ntyp = 3,
ecutwfc = 49 ,
ecutrho = 411 ,
occupations = 'smearing' ,
degauss = 0.05D0 ,
smearing = 'methfessel-paxton' ,
vdw_corr = 'grimme-d2' ,
/
&ELECTRONS
mixing_beta = 0.2D0 ,
diagonalization = 'david' ,
/
&IONS
ion_dynamics = 'verlet' ,
ion_temperature = 'rescaling' ,
tempw = 50 ,
tolp = 1 ,
delta_t = 1 ,
nraise = 1 ,
/
ATOMIC_SPECIES
O 15.99900 O.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.00790 H.pbe-kjpaw_psl.1.0.0.UPF
Pd 106.40000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS angstrom
H 3.749292613 5.567569316 9.134421266
H 3.803720062 4.024397884 9.087662377
O 3.173832077 4.774393547 9.142099838
Pd -0.015321105 9.523398271 6.774164621
Pd 2.722844638 4.758595557 6.785562209
Pd 5.490883134 9.523895908 6.777071069
Pd 8.228806411 4.758298844 6.770864880
Pd 1.356930947 2.368010181 6.769560450
Pd 4.119325735 7.149818888 6.768390428
Pd 6.862178456 2.372021282 6.778917989
Pd 2.738593954 9.523860670 6.777549970
Pd 5.494886254 4.759214643 6.766979210
Pd 1.358442938 7.149196831 6.769444322
Pd 4.118144062 2.368040151 6.768758108
Pd 6.862965497 7.145267601 6.777586390
Pd 0.000000000 6.353486495 4.492593385 0 0 0
Pd 2.751140354 1.588371624 4.492593385 0 0 0
Pd 5.502280707 6.353486495 4.492593385 0 0 0
Pd 8.253421061 1.588371624 4.492593385 0 0 0
Pd 1.375570177 8.736043930 4.492593385 0 0 0
Pd 4.126710530 3.970929059 4.492593385 0 0 0
Pd 6.877850884 8.736043930 4.492593385 0 0 0
Pd 2.751140354 6.353486495 4.492593385 0 0 0
Pd 5.502280707 1.588371624 4.492593385 0 0 0
Pd 1.375570177 3.970929059 4.492593385 0 0 0
Pd 4.126710530 8.736043930 4.492593385 0 0 0
Pd 6.877850884 3.970929059 4.492593385 0 0 0
Pd 0.000000000 3.176743247 2.246296693 0 0 0
Pd 2.751140354 7.941858119 2.246296693 0 0 0
Pd 5.502280707 3.176743247 2.246296693 0 0 0
Pd 8.253421061 7.941858119 2.246296693 0 0 0
Pd 1.375570177 5.559300683 2.246296693 0 0 0
Pd 4.126710530 0.794185812 2.246296693 0 0 0
Pd 6.877850884 5.559300683 2.246296693 0 0 0
Pd 2.751140354 3.176743247 2.246296693 0 0 0
Pd 5.502280707 7.941858119 2.246296693 0 0 0
Pd 1.375570177 0.794185812 2.246296693 0 0 0
Pd 4.126710530 5.559300683 2.246296693 0 0 0
Pd 6.877850884 0.794185812 2.246296693 0 0 0
Pd 0.000000000 9.530229742 0.000000000 0 0 0
Pd 2.751140354 4.765114871 0.000000000 0 0 0
Pd 5.502280707 9.530229742 0.000000000 0 0 0
Pd 8.253421061 4.765114871 0.000000000 0 0 0
Pd 1.375570177 2.382557436 0.000000000 0 0 0
Pd 4.126710530 7.147672307 0.000000000 0 0 0
Pd 6.877850884 2.382557436 0.000000000 0 0 0
Pd 2.751140354 9.530229742 0.000000000 0 0 0
Pd 5.502280707 4.765114871 0.000000000 0 0 0
Pd 1.375570177 7.147672307 0.000000000 0 0 0
Pd 4.126710530 2.382557436 0.000000000 0 0 0
Pd 6.877850884 7.147672307 0.000000000 0 0 0
K_POINTS automatic
4 4 1 0 0 0
------------------
Dr. Jibiao Li,
Department of Material Science and Engineering
Yangtze Normal University
Juxian Dadao 16#, Fuling, Chongqing, China
Email: jibiaoli at yznu.edu.cn, jibiaoli at foxmail.com, jibiao.li at hotmail.com
Homepage: https://www.researchgate.net/profile/Jibiao_Li
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