<div dir="ltr"><div>Dear Natalie, the MD code hasn't significantly changed recently. I get exactly the same results with v.6.41 and with v.6.3 (+ backports). I don't think it is a problem of symmetry either: it's option ion_temperature = 'initial' (an option whose existence I ignored) that doesn't seem to do what it is supposed to do.</div><div><br></div><div>Paolo<br> </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 18, 2019 at 5:57 AM Holzwarth, Natalie <<a href="mailto:natalie@wfu.edu">natalie@wfu.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>I looked into this previously reported problem of the different results with a simple MD run setting the initial temperature in QE 6.4.1 and 6.3 and (as usual) it seems that the explanation may be more complicated. What we have often done is to start from an equilibrium geometry and use the 'initial' key word in the hopes that all atoms will be given a random velocity. In our case, QE detected some symmetry in the atomic positions and apparently zeroed the initial velocities within the routine dynamics_module.f90. Is there a way to suppress this symmetry detection? We did put nosym=.true. but the code seems to have set invsym=.true. anyway. Perhaps it is intended that users should move atoms off of their symmetry positions before running MD simulations? Thanks for your advice about this. Natalie</div><div><br></div><div dir="ltr"><div><div dir="ltr" class="gmail-m_-2623140736646114881gmail_signature">N. A. W. Holzwarth email: <a href="mailto:natalie@wfu.edu" target="_blank">natalie@wfu.edu</a><div>Department of Physics web: <a href="http://www.wfu.edu/~natalie" target="_blank">http://www.wfu.edu/~natalie</a></div><div>Wake Forest University phone: 1-336-758-5510 </div><div>Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab</div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 10, 2019 at 6:29 PM Holzwarth, Natalie <<a href="mailto:natalie@wfu.edu" target="_blank">natalie@wfu.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Quantum Espresso developers,<div> Hopefully this might be something that is easy to track down but I cannot figure it out. We noticed that we cannot set the initial temperature in our md simulations in QE 6.4.1 (or 6.4) in the same way that works fine in QE 6.3. For example, in a simple test , the comparison between the results for " grep temperature *out" is:</div><div> QE 6.3 QE 6.4.1<div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1800.00000000 K temperature = 0.00000000 K </div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1798.79298998 K temperature = 0.00000000 K</div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1795.18924725 K temperature = 0.00000001 K </div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1789.20477087 K temperature = 0.00000002 K</div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1780.85173941 K temperature = 0.00000048 K </div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1770.15802096 K temperature = 0.00000014 K</div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1757.15885289 K temperature = 0.00000032 K </div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1741.89911601 K temperature = 0.00000575 K</div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1724.42918183 K temperature = 0.00001204 K </div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1704.80836203 K temperature = 0.00001108 K</div><div dir="ltr" class="gmail-m_-2623140736646114881gmail-m_8560731894072478280gmail_signature"> temperature = 1683.10589232 K temperature = 0.00000872 K </div><div>The sample input file is pasted below. The only difference between the runs is the version of QE.</div><div> Thanks in advance for your suggestions. Sincerely, Natalie</div><div>-------------------sample input file for md run-----------------------------</div><div><div>#!/bin/tcsh</div><div>#</div><div>#SBATCH --nodes=1</div><div>#SBATCH --ntasks-per-node=8</div><div>#SBATCH --cpus-per-task=1</div><div>#SBATCH --account="natalieGrp"</div><div>#SBATCH --output="JOB-%j.o"</div><div>#SBATCH --error="JOB-%j.e"</div><div>#SBATCH --mail-user=<a href="mailto:natalie@wfu.edu" target="_blank">natalie@wfu.edu</a></div><div>#SBATCH --mail-type=BEGIN,END,FAIL</div><div>#SBATCH --job-name="NaCl"</div><div>#SBATCH --time=0-10:00:00</div><div>#SBATCH --mem=24gb</div><div>#SBATCH --partition=small</div><div>umask 002</div><div># Note: SLURM has no batch input for cputime, excluding.</div><div>#</div><div>source /etc/profile.d/modules.csh</div><div>module purge</div><div>module load rhel7/openmpi/3.1.1-intel-2018</div><div>#</div><div>echo 'hostname' `/bin/hostname`</div><div>echo 'job directory' `pwd`</div><div>#</div><div>setenv TMPDIR /scratch/$SLURM_JOBID</div><div>echo 'Reset TMPDIR for this job to ' $TMPDIR</div><div><br></div><div>set PW=/home/natalie/EL7/publiccode/QE/qe-6.4.1/bin/pw.x</div><div><br></div><div>#NOTE:SLURM defaults to running jobs in the directory where submitted;</div><div>#NOTE:Consider --workdir directive instead; and check functionality!</div><div>cd ${SLURM_SUBMIT_DIR}</div><div><br></div><div>cat > NaCl.in << EOF </div><div><br></div><div>&CONTROL</div><div> calculation = "md",</div><div> pseudo_dir = '/deac/natalieGrp/wfurc9/natalie/EL6/rc9/PAWatoms/poscorenhat/',</div><div> verbosity = "high",</div><div> outdir = "$TMPDIR/",</div><div> prefix = "conv",</div><div> restart_mode = 'from_scratch',</div><div> nstep = 30,</div><div> dt = 20,</div><div> forc_conv_thr = 1.0D-5,</div><div> etot_conv_thr = 1.0D-6,</div><div> tstress = .true.,</div><div> tprnfor = .true.,</div><div>/</div><div>&SYSTEM</div><div> ibrav = 1,</div><div> celldm(1)=1.0331018E+01,</div><div> nat = 8,</div><div> ntyp = 2,</div><div> nosym =.TRUE.,</div><div> ecutwfc = 64.D0,</div><div> use_all_frac = .TRUE.,</div><div> occupations = "smearing",</div><div> smearing = "gaussian",</div><div> degauss = 0.001D0,</div><div>/</div><div>&ELECTRONS</div><div> conv_thr = 1.D-8,</div><div> electron_maxstep = 200,</div><div>/</div><div>&IONS</div><div> ion_dynamics = 'verlet',</div><div> ion_temperature = 'initial',</div><div> tempw = 1800.d0,</div><div> pot_extrapolation = 'second-order',</div><div> wfc_extrapolation = 'second-order',</div><div>/</div><div>&CELL</div><div> cell_dynamics='none',</div><div> wmass = 1.0,</div><div> press = 0.0,</div><div>/</div><div>ATOMIC_SPECIES</div><div>Na 22.989769 Na.LDA-PW-paw.UPF</div><div>Cl 35.45 Cl.LDA-PW-paw.UPF</div><div>ATOMIC_POSITIONS {crystal}</div><div>Na 0.000000000 0.000000000 0.000000000</div><div>Na 0.500000000 0.500000000 0.000000000</div><div>Na 0.000000000 0.500000000 0.500000000</div><div>Na 0.500000000 0.000000000 0.500000000</div><div>Cl 0.500000000 0.500000000 0.500000000</div><div>Cl 0.000000000 0.000000000 0.500000000</div><div>Cl 0.500000000 0.000000000 0.000000000</div><div>Cl 0.000000000 0.500000000 0.000000000</div><div>K_POINTS AUTOMATIC</div><div>2 2 2 1 1 1</div><div>EOF</div><div><br></div><div>mpirun $PW -in NaCl.in > NaCl.out</div></div><div><br></div><div>-------------------------------------------------------------------------------------</div><div><br></div><div>N. A. W. Holzwarth email: <a href="mailto:natalie@wfu.edu" target="_blank">natalie@</a> <br></div><div>Department of Physics web: <a href="http://www.wfu.edu/~natalie" target="_blank">http://www.wfu.edu/~natalie</a></div><div>Wake Forest University phone: 1-336-758-5510 </div><div>Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab</div></div></div></div></div></div></div>
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