[QE-users] Difference in phonon frequencies produced by matdyn.x
-0.00 0.568969 -0.00-0.011697 -0.00 )* * ( -0.097317 -0.00 0.568969 -0.00-0.011697 -0.00 )* * ( -0.097317 -0.00 0.568969 -0.00-0.011697 0.00 )* * freq (4) = 5.235913 [THz] = 174.651242 [cm-1]* * ( -0.25 0.00 0.246235 0.00-0.00 -0.00 )* * ( 0.70 -0.00-0.685335 -0.00 0.00 0.00 )* * ( 0.70 -0.00-0.685335 -0.00 0.00 0.00 )* * freq (5) = 5.235913 [THz] = 174.651242 [cm-1]* * ( 0.246234 0.000623 0.25 0.00 0.00 -0.00 )* * ( -0.685333 -0.001733-0.70 -0.00-0.00 -0.00 )* * ( -0.685333 -0.001733-0.70 -0.00 0.00 0.00 )* * freq (6) = 7.799484 [THz] = 260.162777 [cm-1]* * ( 0.00 -0.00 0.00 0.00 0.00 0.00 )* * ( 0.707105 -0.10 0.001673 -0.00-0.00 -0.00 )* * ( -0.707105 0.10-0.001673 0.00-0.00 0.00 )* * freq (7) = 7.799484 [THz] = 260.162777 [cm-1]* * ( 0.00 -0.00-0.00 -0.00-0.00 0.00 )* * ( 0.001673 0.00-0.707105 -0.00 0.00 -0.00 )* * ( -0.001673 -0.00 0.707105 0.00 0.00 0.00 )* * freq (8) = 9.672630 [THz] = 322.644206 [cm-1]* * ( 0.00 0.00-0.00 0.00-0.246235 0.00 )* * ( 0.00 -0.00 0.00 0.00 0.685335 -0.00 )* * ( -0.00 0.00 0.00 -0.00 0.685335 0.00 )* * freq (9) = 10.162710 [THz] = 338.991522 [cm-1]* * ( -0.00 -0.00-0.00 0.00-0.00 -0.00 )* * ( -0.00 -0.00 0.00 0.00-0.707107 0.00 )* * ( 0.00 -0.00-0.00 0.00 0.707107 0.00 )* * *** I summarize the phonon frequencies for easier comparison: *Gamma-M-K-Gamma:* -0.0.0. 174.6512 260.1628 260.1628 305.6148 305.9012 338.9915 *DOS: *-0. -0.0. 174.6512 174.6512 260.1628 260.1628 322.6442 338.9915 As can be seen, the phonon calculation along high symmetry point shows a degenerate frequency at *260.1628* while the DOS calculation shows degeneracy at *174.6512 *and *260.1628.* Moreover, a new phonon mode with frequency *322.6442 *appears in the DOS calculation that is absent from calculation along high symmetry directions. Why should the Gamma point frequency depend on the list of kpoints one is diagonalizing dynamical matrices on? It does not seem to be numerical error since the difference is so huge. Can anyone help me understand it? Thank you very much FYI, input file for ph.x is shown below: *phonons of HfS2 ='Hf'epsil=.true.fildyn='HfS2.dyn', outdir='./tmp/'tr2_ph=1.0d-12 ldisp=.true nq1=4 nq2=4 nq3=4 /* -- 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Cell temperature in NPT simulations using cp.x
of lattice structure at the initial state. This observation leads me to believe that it is kind of like a pulse of kinetic energy injected into the system that quickly get distributed among atoms equally. But is it normal for the ionic temperature to reach as high as 5000K? I know I have a long list of questions here. I would greatly appreciate if you can provide any suggestions to me!! Thank you very much in advance. Best -- -------- 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] NVE simulation in cp.x - large fluctuation in temperature
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: >> >> >> calculation='cp', >> title='Halfnium disulfide' >> restart_mode='restart', >> ndr=53, >> ndw=54, >> nstep=5, >> 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/', >> / >> >> 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 >> / >> >> electron_dynamics='verlet' >> electron_velocities='zero' >> emass=400 >> emass_cutoff=1 >> / >> >> ion_dynamics = 'verlet' >> ion_damping=0.1 >> !ion_nstepe=10 >> / >> >> 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 -0.0 -0.0
[QE-users] NVE simulation in cp.x - large fluctuation in temperature
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 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: ** *calculation='cp',* *title='Halfnium disulfide'* *restart_mode='restart',* *ndr=53,* *ndw=54,* *nstep=5,* *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/',* * /* * * *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* */* * * *electron_dynamics='verlet'* *electron_velocities='zero'* *emass=400* *emass_cutoff=1* */* * * *ion_dynamics = 'verlet'* *ion_damping=0.1* *!ion_nstepe=10* * /* * * *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 -0.0 -0.0 -0.0* *S0.7 0.3 0.257234636* *S0.3 0.7 -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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Large difference between lattice structure simulated by pwscf code and cp.x code
rstand the discrepancy I see in the results produced by pw.x and cp.x code? Or pointing out any mistake I have made during my simulations? Thank you in advance for your help, sincerely! 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [Pw_forum] Phonon of single layer MoS2
Dear All: Please allow me to apologize for my previous behaviour. It was inappropriate, immature and lacked the respect you deserved. It was embarrassing, but I learned that nobody appreciated my poor behaviour. In the future, I will learn to adjust my behaviour befitting the environment and situation. Again, I am terribly sorry for my actions. Best wishes to you. Sincerely, Jie Peng PhD student, Mechanical Engineering Department, University of Maryland > On Jul 14, 2015, at 07:00, Suza W <suza@gmail.com> wrote: > > Dear All, > > Reply To A Public Reply : > > Politeness is such a lonely word in the underdeveloped world where people > ignore Birth Control; > and for a better world, contraception is extremely needed to control both > population explosion and explosion of scientific papers :) > > I am sorry as my post sounds quite off-topic for this forum. > > With best regards, > > Suza W. > Assistant Professor, > Kakatiya University. > > > On Tue, Jul 14, 2015 at 10:07 AM, Nicola Marzari <nicola.marz...@epfl.ch > <mailto:nicola.marz...@epfl.ch>> wrote: > > > Dear Jie Peng, > > > a public reply: > > 1) please use some amount of politeness in replying (e.g. Dear Nicola, > many thanks for your comments. I have tried them out, etc...) > > 2) you have had 3 people reply to your comments. The least you can do > is try to understand what you are doing, and report. The fact that > to you 6x6x6 or 3x3x1 sampling makes no difference means to all of > us zero understanding. My suggestion would be to change research field. > > 3) please sign with your affiliation. > > > nicola > > > > On 14/07/2015 04:56, Shopping wrote: > > Yeah, I have tried this, but it seems to make no difference, still a log > > time to run. > > > > > > Best > > Jie Peng > > > > -- > > -- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > Director, National Centre for Competence in Research NCCR MARVEL, EPFL > ___ > Pw_forum mailing list > Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org> > http://pwscf.org/mailman/listinfo/pw_forum > <http://pwscf.org/mailman/listinfo/pw_forum> > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
