[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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