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 <[email protected]> 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 / [email protected] / 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: [email protected] >> >> >> > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > -- ------------------------------------------------------------------------------------------------------------------------ Jie Peng PhD student 2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland College Park, Maryland, USA Phone:(+1) 240-495-9445 Email: [email protected]
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