Ari:

Indeed! You are right on spot. The too small size unit cell that leads to
inaccurate structure and energy is responsible for large temperature
fluctuation here.

I am trying to increase the size of the supercell now.

Thanks!

On Sat, Apr 14, 2018 at 6:06 AM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
wrote:

>
> 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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-- 
------------------------------------------------------------------------------------------------------------------------
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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