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<span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Dear all:</span><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">I have been running Molecular dynamics simulations on NPT assemble of HfS2.</div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">The starting configuration has already been relaxed by consecutive steps of electron relaxation, ion relaxation, and cell relaxation. As CPMD in quantum espresso uses Gamma point only wavefunction sampling, an accurate calculation of structure and energy requires usage of a large supercell. Therefore I carried out NPT simulations of a 2*2*2 and 3*3*3 HfS2 supercell, containing 24 and 81 atoms respectively. The input file and results are attached below:</div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><b>For 2*2*2 supercell</b><br clear="all"><div><div><div><i>&control</i></div><div><i> calculation='vc-cp',</i></div><div><i> restart_mode='restart',</i></div><div><i> tstress = .true.</i></div><div><i> tprnfor = .true.</i></div><div><i> ndr=54</i></div><div><i> ndw=55</i></div><div><i> nstep=40000</i></div><div><i> dt=10</i></div><div><i> etot_conv_thr=1e-6</i></div><div><i> forc_conv_thr=1e-3</i></div><div><i> ekin_conv_thr=1e-5</i></div><div><i> wf_collect=.true.</i></div><div><i> prefix='HfS2',</i></div><div><i> pseudo_dir='/home/jpeng/HfS2/<wbr>potential'</i></div><div><i> outdir='./tmp/',</i></div><div><i> /</i></div><div><i> &system</i></div><div><i> ibrav= 4,</i></div><div><i> a=7.3058</i></div><div><i> c=11.3088</i></div><div><i> nat=24, ntyp= 2,</i></div><div><i> ecutwfc =50</i></div><div><i> vdw_corr='DFT-D',</i></div><div><i> ! lspinorb=.true.</i></div><div><i> ! noncolin=.true.</i></div><div><i> ! ecutrho=300</i></div><div><i> ! nbnd=14</i></div><div><i>! occupations='smearing'</i></div><div><i>! smearing='gaussian'</i></div><div><i>! degauss=0.01</i></div><div><i> ! nspin=2</i></div><div><i> ! starting_magnetization(1)=0.1</i></div><div><i>/</i></div><div><i> &electrons</i></div><div><i> electron_dynamics='verlet'</i></div><div><i>! electron_velocities='zero'</i></div><div><i> emass=400</i></div><div><i> emass_cutoff=1</i></div><div><i>/</i></div><div><i> &ions</i></div><div><i> ion_dynamics = 'verlet'</i></div><div><i> ion_temperature='nose'</i></div><div><i>! ion_damping=0.1</i></div><div><i> tempw=300</i></div><div><i> fnosep=6</i></div><div><i>! ion_nstepe=10</i></div><div><i> /</i></div><div><i> &cell</i></div><div><i> cell_dynamics = 'pr'</i></div><div><i> </i></div><div><i>/</i></div><div><i>ATOMIC_SPECIES</i></div><div><i> Hf 178.49 Hf.pbe-mt_fhi.UPF</i></div><div><i> S 32.065 S.pbe-mt_fhi.UPF</i></div><div><i>ATOMIC_POSITIONS angstrom</i></div><div><i>(atom position list)</i></div></div></div><div><i><br></i></div><div><i><br><br></i></div><div><i><br></i></div><div><b>For 3*3*3 supercell</b></div><div><div><i>&control</i></div><div><i> calculation='vc-cp',</i></div><div><i> restart_mode='restart',</i></div><div><i> tstress = .true.</i></div><div><i> tprnfor = .true.</i></div><div><i> ndr=54</i></div><div><i> ndw=55</i></div><div><i> nstep=40000</i></div><div><i> dt=10</i></div><div><i> etot_conv_thr=1e-6</i></div><div><i> forc_conv_thr=1e-3</i></div><div><i> ekin_conv_thr=1e-5</i></div><div><i> wf_collect=.true.</i></div><div><i> prefix='HfS2',</i></div><div><i> pseudo_dir='/home/jpeng/HfS2/<wbr>potential'</i></div><div><i> outdir='./tmp/',</i></div><div><i> /</i></div><div><i> &system</i></div><div><i> ibrav= 4,</i></div><div><i> a=10.9587</i></div><div><i> c=16.9632</i></div><div><i> nat=81, ntyp= 2,</i></div><div><i> ecutwfc =50</i></div><div><i> vdw_corr='DFT-D',</i></div><div><i> ! lspinorb=.true.</i></div><div><i> ! noncolin=.true.</i></div><div><i> ! ecutrho=300</i></div><div><i> ! nbnd=14</i></div><div><i>! occupations='smearing'</i></div><div><i>! smearing='gaussian'</i></div><div><i>! degauss=0.01</i></div><div><i> ! nspin=2</i></div><div><i> ! starting_magnetization(1)=0.1</i></div><div><i>/</i></div><div><i> &electrons</i></div><div><i> electron_dynamics='verlet'</i></div><div><i>! electron_velocities='zero'</i></div><div><i> emass=800</i></div><div><i> emass_cutoff=1</i></div><div><i>/</i></div><div><i> &ions</i></div><div><i> ion_dynamics = 'verlet'</i></div><div><i> ion_temperature='nose'</i></div><div><i>! ion_damping=0.1</i></div><div><i> tempw=300</i></div><div><i> fnosep=6</i></div><div><i>! ion_nstepe=10</i></div><div><i> /</i></div><div><i> &cell</i></div><div><i> cell_dynamics = 'pr'</i></div><div><i> </i></div><div><i>/</i></div><div><i><br></i></div><div><i>ATOMIC_SPECIES</i></div><div><i> Hf 178.49 Hf.pbe-mt_fhi.UPF</i></div><div><i> S 32.065 S.pbe-mt_fhi.UPF</i></div><div><i>ATOMIC_POSITIONS angstrom</i></div><div><i>(atom position list)</i></div></div><div><br></div><div><br></div><div>The temperature is set to 300K, the system is connected to a Nose-Hoover thermostate to equilibrate. The pressure is set to 0.</div><div><br></div><div>I attache the results of temph and tempp printed out in the output files below. The inset is a zoom in of the period I think the system has reached equilibrium.</div><div>For 2*2*2 supercell</div><div><br></div><div><img src="cid:ii_jgdt6eev6_162f835f36719e5a" width="480" height="288"></div><div><img src="cid:ii_jgdt6ikr7_162f8360777db27c" width="481" height="288"><br><br><br><br><br><br><br></div><div><br></div><div>For a 3*3*3 supercell</div><div><br></div><div><img src="cid:ii_jgdt6zp68_162f8365f96aeb11" width="480" height="288"><br><br></div><div><img src="cid:ii_jgdt73ia9_162f83670ad5631a" width="480" height="288"><br><br><br><br><br></div><div><br></div><div>There are lots of thoughts and doubts here:</div><div><br></div><div>1. Has the system reached equilibrium? I consider the system to be in equilibrium as I see a stable variation of ionic temperature around the desired temperature 300K, is it enough to support the conclusion that the system is in equilibrium? I know that the total energy, kinetic energy of the system are also oscillating around a constant value. What other behaviors or quantities can further consolidate this conclusion?</div><div><br>2. What is the temph, or the fictitious cell temperature? I have read the paper <span style="font-style:italic;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:13px;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Bernasconi, M., G. L. Chiarotti, P. Focher, S. Scandolo, E. Tosatti, and M. Parrinello. "First-principle-constant pressure molecular dynamics." </span><span style="font-style:italic;color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:13px;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">Journal of Physics and Chemistry of Solids</span><span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:13px;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="font-style:italic"> </span><i>56, no. 3-4 (1995): 501-505,<span> </span></i>on which I think the variable cell CPMD in quantum espresso is built on. There is no fictitious cell temperature in the paper, but I infer that would be the temperature corresponding to the kinetic energy of the cell, which is sth like 1/2*KB*T=1/2*W*Tr(dh'/dt*dh/<wbr>dt) where W is the fictitious cell mass, h is the cell vectors. Is it correct? What is the unit for the fictitious cell temperature? How come it can be as high as, for instance 8000 for a 3*3*3* supercell NPT simulation?</span></div><div><font face="Arial, sans-serif"><br></font></div><div><font face="Arial, sans-serif">3. How to reduce variations of the temperature? Right now I have ionic temperature varying between 150K to 550 K for a 2*2*2 supercell while 180K to 420K for a 3*3*3 supercell. How do I reduce the temperature variations? Any general suggestions?</font></div><div><font face="Arial, sans-serif"><br></font></div><div><font face="Arial, sans-serif">4. The initial "jump" in cell and ionic temperature. In both NPT simulations for 2*2*2 and 3*3*3 supercell, there is a huge jump in the temperature values at the initial stage. However, I take a look at the animation of the atom positions and cell shapes during the entire NPT simulation, there is no significant change 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. <span style="color:rgb(34,34,34);font-family:Arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">But is it normal for the ionic temperature to reach as high as 5000K?</span></font></div><div><br></div><div>I know I have a long list of questions here. I would greatly appreciate if you can provide any suggestions to me!!</div><div><br></div><div>Thank you very much in advance.<br><br></div><div>Best</div></div>
<br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div style="font-size:12.8px">------------------------------------------------------------------------------------------------------------------------<br>Jie Peng</div><div style="font-size:12.8px">PhD student<br>2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland<br>College Park, Maryland, USA<br>Phone:(+1) 240-495-9445<br></div><div style="font-size:12.8px">Email: <a href="mailto:jiepeng@umd.edu" target="_blank">jiepeng@umd.edu</a><br></div></div><div><br></div></div></div>
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