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.
Paolo On Thu, Apr 18, 2019 at 5:57 AM Holzwarth, Natalie <nata...@wfu.edu> wrote: > 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 > > N. A. W. Holzwarth email: > nata...@wfu.edu > Department of Physics web: > http://www.wfu.edu/~natalie > Wake Forest University phone: > 1-336-758-5510 > Winston-Salem, NC 27109 USA office: Rm. 300 Olin > Physical Lab > > > On Wed, Apr 10, 2019 at 6:29 PM Holzwarth, Natalie <nata...@wfu.edu> > wrote: > >> Dear Quantum Espresso developers, >> 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: >> QE 6.3 QE 6.4.1 >> temperature = 1800.00000000 K temperature = >> 0.00000000 K >> temperature = 1798.79298998 K temperature = >> 0.00000000 K >> temperature = 1795.18924725 K temperature = >> 0.00000001 K >> temperature = 1789.20477087 K temperature = >> 0.00000002 K >> temperature = 1780.85173941 K temperature = >> 0.00000048 K >> temperature = 1770.15802096 K temperature = >> 0.00000014 K >> temperature = 1757.15885289 K temperature = >> 0.00000032 K >> temperature = 1741.89911601 K temperature = >> 0.00000575 K >> temperature = 1724.42918183 K temperature = >> 0.00001204 K >> temperature = 1704.80836203 K temperature = >> 0.00001108 K >> temperature = 1683.10589232 K temperature = >> 0.00000872 K >> The sample input file is pasted below. The only difference between the >> runs is the version of QE. >> Thanks in advance for your suggestions. Sincerely, Natalie >> -------------------sample input file for md >> run----------------------------- >> #!/bin/tcsh >> # >> #SBATCH --nodes=1 >> #SBATCH --ntasks-per-node=8 >> #SBATCH --cpus-per-task=1 >> #SBATCH --account="natalieGrp" >> #SBATCH --output="JOB-%j.o" >> #SBATCH --error="JOB-%j.e" >> #SBATCH --mail-user=nata...@wfu.edu >> #SBATCH --mail-type=BEGIN,END,FAIL >> #SBATCH --job-name="NaCl" >> #SBATCH --time=0-10:00:00 >> #SBATCH --mem=24gb >> #SBATCH --partition=small >> umask 002 >> # Note: SLURM has no batch input for cputime, excluding. >> # >> source /etc/profile.d/modules.csh >> module purge >> module load rhel7/openmpi/3.1.1-intel-2018 >> # >> echo 'hostname' `/bin/hostname` >> echo 'job directory' `pwd` >> # >> setenv TMPDIR /scratch/$SLURM_JOBID >> echo 'Reset TMPDIR for this job to ' $TMPDIR >> >> set PW=/home/natalie/EL7/publiccode/QE/qe-6.4.1/bin/pw.x >> >> #NOTE:SLURM defaults to running jobs in the directory where submitted; >> #NOTE:Consider --workdir directive instead; and check functionality! >> cd ${SLURM_SUBMIT_DIR} >> >> cat > NaCl.in << EOF >> >> &CONTROL >> calculation = "md", >> pseudo_dir = >> '/deac/natalieGrp/wfurc9/natalie/EL6/rc9/PAWatoms/poscorenhat/', >> verbosity = "high", >> outdir = "$TMPDIR/", >> prefix = "conv", >> restart_mode = 'from_scratch', >> nstep = 30, >> dt = 20, >> forc_conv_thr = 1.0D-5, >> etot_conv_thr = 1.0D-6, >> tstress = .true., >> tprnfor = .true., >> / >> &SYSTEM >> ibrav = 1, >> celldm(1)=1.0331018E+01, >> nat = 8, >> ntyp = 2, >> nosym =.TRUE., >> ecutwfc = 64.D0, >> use_all_frac = .TRUE., >> occupations = "smearing", >> smearing = "gaussian", >> degauss = 0.001D0, >> / >> &ELECTRONS >> conv_thr = 1.D-8, >> electron_maxstep = 200, >> / >> &IONS >> ion_dynamics = 'verlet', >> ion_temperature = 'initial', >> tempw = 1800.d0, >> pot_extrapolation = 'second-order', >> wfc_extrapolation = 'second-order', >> / >> &CELL >> cell_dynamics='none', >> wmass = 1.0, >> press = 0.0, >> / >> ATOMIC_SPECIES >> Na 22.989769 Na.LDA-PW-paw.UPF >> Cl 35.45 Cl.LDA-PW-paw.UPF >> ATOMIC_POSITIONS {crystal} >> Na 0.000000000 0.000000000 0.000000000 >> Na 0.500000000 0.500000000 0.000000000 >> Na 0.000000000 0.500000000 0.500000000 >> Na 0.500000000 0.000000000 0.500000000 >> Cl 0.500000000 0.500000000 0.500000000 >> Cl 0.000000000 0.000000000 0.500000000 >> Cl 0.500000000 0.000000000 0.000000000 >> Cl 0.000000000 0.500000000 0.000000000 >> K_POINTS AUTOMATIC >> 2 2 2 1 1 1 >> EOF >> >> mpirun $PW -in NaCl.in > NaCl.out >> >> >> ------------------------------------------------------------------------------------- >> >> N. A. W. Holzwarth email: natalie@ >> <nata...@wfu.edu> >> Department of Physics web: >> http://www.wfu.edu/~natalie >> Wake Forest University phone: >> 1-336-758-5510 >> Winston-Salem, NC 27109 USA office: Rm. 300 Olin >> Physical Lab >> > _______________________________________________ > Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
_______________________________________________ Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users