[QE-users] Change in temperature control for md simulation in QE 6.4.1 compared with 6.3 -- perhaps instead an issue with detecting symmetry??

[Holzwarth, Natalie]

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:
natalie at 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 <natalie at 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=natalie at 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@
> <natalie at 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20190417/6a553431/attachment.html>