Dear Jie,

  I do not know about the other options, but

1) simulating a periodic system of only three atoms with only the Gamma point cannot lead to an accurate description of the electronic structure, and thus the forces on the ionic cores,

2) the standard deviation in the fluctuations is supposed to be ~sqrt[2/(3*N_atoms)) * T_average ~= 350 K in your case, and the instantaneous fluctuations are of course larger

  Just my quick thoughts...

    Greetings from Sunny Zurich,

       apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
    Ecole Normale Supérieure (ENS), Département de Chimie, Paris
    Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


On Fri, 13 Apr 2018, Jie Peng wrote:

Dear all
I have been running MD simulations on HfS2 using cp.x code in Quantum espresso. 
I start from initial
configuration obtained from pwscf vc-relax, and relax the system using cp.x by 
consecutive steps of:
electron relaxation->ionic relaxation->cell relaxation. Then, I just directly 
start a NVE simulation
starting from the equilibrium configuration. I expect the system to almost stay 
stationary or the
temperature should be very small since I am allowing dynamics in a system that 
is already in
equilibrium. However, what I see is a huge fluctuation in the tmpp output of 
cp.x, as I attach a figure
showing variation of tmpp (Ionic temperature) with simulation time
[IMAGE]

I did this because it is suggested in the user guide you should apply an 
initial displacement to the
atoms in your system after the relaxation since otherwise there will not be any 
dynamics. But what I
see here is a large fluctuation of the system temperature.

The thinking or questions here are

1.Does the tmpp represents the physical temperature of the system here? I think 
it should be since it
is the temperature corresponding to kinetic energy of the ions.

2.It above point is true, why is the temperature varying so fiercely? Am I 
setting incorrect
parameters, for instance the timestep or the fictitious mass? But I took those 
from previous simulation
steps where I did the relaxation, and they all worked well since they 
successfully drived my system to
equilibrium, satisfying the convergence threshold on total energy, forces 
acting on atoms, and the
fictitious electron kinetic energy. I am confused at this point.

The input file for NVE simulation is attached here:

&control
    calculation='cp',
    title='Halfnium disulfide'
    restart_mode='restart',
    ndr=53,
    ndw=54,
    nstep=50000,
    iprint=10
    isave=100,
    tstress = .true.
    tprnfor = .true.
    dt=10,
    wf_collect=.true.
    etot_conv_thr=1e-6
    forc_conv_thr=1e-3
    ekin_conv_thr=1e-5
    prefix='HfS2',
    pseudo_dir='/home/jpeng/HfS2/potential'
    outdir='./tmp/',
 /
 &system
    ibrav= 4,
    a=3.6529
   c=5.6544
    nat=  3, ntyp= 2,
    ecutwfc =50
    vdw_corr='DFT-D',
 !   lspinorb=.true.
 !   noncolin=.true.
 !   ecutrho=300
 !   nbnd=14
!    occupations='smearing'
!    smearing='gaussian'
!   degauss=0.01
 !  nspin=2
 !   starting_magnetization(1)=0.1
! Hf  95.94  Hf.pbe-mt_fhi.UPF
! S  32.065  S.pbe-mt_fhi.UPF
/
 &electrons
    electron_dynamics='verlet'
    electron_velocities='zero'
    emass=400
    emass_cutoff=1
/
 &ions
    ion_dynamics = 'verlet'
    ion_damping=0.1
!    ion_nstepe=10
 /
 &cell
    cell_dynamics = 'none'
 
/
ATOMIC_SPECIES
 Hf  95.94  Hf.pbe-mt_fhi.UPF
 S  32.065  S.pbe-mt_fhi.UPF
ATOMIC_POSITIONS (crystal)
Hf      -0.000000000  -0.000000000  -0.000000000
S        0.666666667   0.333333333   0.257234636
S        0.333333333   0.666666667  -0.257234636

Anyone could help me on it? Thank you very much.

Best
Jie
--
------------------------------------------------------------------------------------------------------
------------------
Jie Peng
PhD student
2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland
College Park, Maryland, USA
Phone:(+1) 240-495-9445
Email: jiep...@umd.edu


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