<div dir="ltr">Ari:<div><br></div><div>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.</div><div><br></div><div>I am trying to increase the size of the supercell now.</div><div><br></div><div>Thanks!</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Apr 14, 2018 at 6:06 AM, Ari P Seitsonen <span dir="ltr"><<a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Dear Jie,<br>
<br>
I do not know about the other options, but<br>
<br>
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,<br>
<br>
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<br>
<br>
Just my quick thoughts...<br>
<br>
Greetings from Sunny Zurich,<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=<wbr>*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=<wbr>-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" rel="noreferrer" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Supérieure (ENS), Département de Chimie, Paris<br>
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<span class=""><br>
<br>
<br>
On Fri, 13 Apr 2018, Jie Peng wrote:<br>
<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
Dear all<br>
I have been running MD simulations on HfS2 using cp.x code in Quantum espresso. I start from initial<br>
configuration obtained from pwscf vc-relax, and relax the system using cp.x by consecutive steps of:<br>
electron relaxation->ionic relaxation->cell relaxation. Then, I just directly start a NVE simulation<br>
starting from the equilibrium configuration. I expect the system to almost stay stationary or the<br>
temperature should be very small since I am allowing dynamics in a system that is already in<br>
equilibrium. However, what I see is a huge fluctuation in the tmpp output of cp.x, as I attach a figure<br>
showing variation of tmpp (Ionic temperature) with simulation time<br></span>
[IMAGE]<div><div class="h5"><br>
<br>
I did this because it is suggested in the user guide you should apply an initial displacement to the<br>
atoms in your system after the relaxation since otherwise there will not be any dynamics. But what I<br>
see here is a large fluctuation of the system temperature.<br>
<br>
The thinking or questions here are<br>
<br>
1.Does the tmpp represents the physical temperature of the system here? I think it should be since it<br>
is the temperature corresponding to kinetic energy of the ions.<br>
<br>
2.It above point is true, why is the temperature varying so fiercely? Am I setting incorrect<br>
parameters, for instance the timestep or the fictitious mass? But I took those from previous simulation<br>
steps where I did the relaxation, and they all worked well since they successfully drived my system to<br>
equilibrium, satisfying the convergence threshold on total energy, forces acting on atoms, and the<br>
fictitious electron kinetic energy. I am confused at this point.<br>
<br>
The input file for NVE simulation is attached here:<br>
<br>
&control<br>
calculation='cp',<br>
title='Halfnium disulfide'<br>
restart_mode='restart',<br>
ndr=53,<br>
ndw=54,<br>
nstep=50000,<br>
iprint=10<br>
isave=100,<br>
tstress = .true.<br>
tprnfor = .true.<br>
dt=10,<br>
wf_collect=.true.<br>
etot_conv_thr=1e-6<br>
forc_conv_thr=1e-3<br>
ekin_conv_thr=1e-5<br>
prefix='HfS2',<br>
pseudo_dir='/home/jpeng/HfS2/p<wbr>otential'<br>
outdir='./tmp/',<br>
/<br>
&system<br>
ibrav= 4,<br>
a=3.6529<br>
c=5.6544<br>
nat= 3, ntyp= 2,<br>
ecutwfc =50<br>
vdw_corr='DFT-D',<br>
! lspinorb=.true.<br>
! noncolin=.true.<br>
! ecutrho=300<br>
! nbnd=14<br>
! occupations='smearing'<br>
! smearing='gaussian'<br>
! degauss=0.01<br>
! nspin=2<br>
! starting_magnetization(1)=0.1<br>
! Hf 95.94 Hf.pbe-mt_fhi.UPF<br>
! S 32.065 S.pbe-mt_fhi.UPF<br>
/<br>
&electrons<br>
electron_dynamics='verlet'<br>
electron_velocities='zero'<br>
emass=400<br>
emass_cutoff=1<br>
/<br>
&ions<br>
ion_dynamics = 'verlet'<br>
ion_damping=0.1<br>
! ion_nstepe=10<br>
/<br>
&cell<br>
cell_dynamics = 'none'<br>
<br>
/<br>
ATOMIC_SPECIES<br>
Hf 95.94 Hf.pbe-mt_fhi.UPF<br>
S 32.065 S.pbe-mt_fhi.UPF<br>
ATOMIC_POSITIONS (crystal)<br>
Hf -0.000000000 -0.000000000 -0.000000000<br>
S 0.666666667 0.333333333 0.257234636<br>
S 0.333333333 0.666666667 -0.257234636<br>
<br>
Anyone could help me on it? Thank you very much.<br>
<br>
Best<br>
Jie<br>
--<br>
------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------<br>
------------------<br>
Jie Peng<br>
PhD student<br>
2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland<br>
College Park, Maryland, USA<br>
Phone:(+1) 240-495-9445<br>
Email: <a href="mailto:jiepeng@umd.edu" target="_blank">jiepeng@umd.edu</a><br>
<br>
<br>
</div></div></blockquote>
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