Dear Jie Peng, suppose you were running a model harmonic system in 1 dimension.

M a = - K x at fixed energy E.

`The kinetic energy would fluctuate harmonically between 0 (at`

`maximum/minimum elongation) and E at the equilibrium distance .`

`On average the Kinetic energy would be E/2 and its fluctuation some`

`big fraction of E^2`

`Something like sigma^2 = 1/T \int_0^T (E cos^2(2pi t/T) -E/2)^2 dt =`

`E^2 1/T \int_0^T (cos(4pi t/T)/2)^2 dt = (E/2)^2 1/2pi \int_0^2pi`

`cos^2(x) dx = (E/2)^2 / 2`

or sigma = 1/sqrt(2) * E/2 = 1/sqrt(2) avg EKin

`with 1 degree of freedom the mean square fluctuation of the kinetic`

`energy is 70% of its average !`

`you have 3 atoms in your cell hence 9 degrees of freedom. Assuming`

`each contributes independently to the average this goes down by a factor`

`1/sqrt(9)=1/3`

`actually more likely just 1/sqrt(6) as the total momentum is`

`conserved so only 6 modes at Gamma are actually excited...`

`If you perform your simulation in a bigger supercell with more atoms`

`(more degrees of freedom) the average will be more stable (`

`proportionally to 1/sqrt(#deg.of.freedom-3 ) ... moreover the thermal`

`excitations of vibrational modes will be sampled more faithfully.`

best stefano On 13/04/2018 21:39, Jie Peng wrote:

Dear allI have been running MD simulations on HfS2 using cp.x code in Quantumespresso. I start from initial configuration obtained from pwscfvc-relax, and relax the system using cp.x by consecutive steps of:electron relaxation->ionic relaxation->cell relaxation. Then, I justdirectly start a NVE simulation starting from the equilibriumconfiguration. I expect the system to almost stay stationary or thetemperature should be very small since I am allowing dynamics in asystem that is already in equilibrium. However, what I see is a hugefluctuation in the /tmpp/ output of cp.x, as I attach a figure showingvariation of tmpp (Ionic temperature) with simulation timeI did this because it is suggested in the user guide you should applyan initial displacement to the atoms in your system after therelaxation since otherwise there will not be any dynamics. But what Isee here is a large fluctuation of the system temperature.The thinking or questions here are1.Does the tmpp represents the physical temperature of the systemhere? I think it should be since it is the temperature correspondingto 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 thefictitious mass? But I took those from previous simulation steps whereI did the relaxation, and they all worked well since they successfullydrived my system to equilibrium, satisfying the convergence thresholdon total energy, forces acting on atoms, and the fictitious electronkinetic 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 <mailto:jiep...@umd.edu> _______________________________________________ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users

_______________________________________________ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users