[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??
Lorenzo Paulatto
paulatz at gmail.com
Thu Apr 18 11:11:25 CEST 2019
> symmetry detection? We did put nosym=.true. but the code seems to
> have set invsym=.true. anyway.
I see what you mean,
with the exact same input version 6.3 set the variable invsym, from
symm_base to false, while the current version sets it to true.
This breaks start_therm because the only possible initial velocities
that respect the constraint in this case are all zero.
The bug is that version 6.3 sets invsym AFTER enforcing nosym=.true.,
while git version sets invsym BEFORE enforcing nosym=.true., the
subroutine find_sym is identical
The change seems to have occurred in commit 23fb73f9b7 inside
PW/src/setup.f90 I'll let Paolo Giannozzi have a look before going
deeper, as I do not immediately understand what has changed, I think it
has something to do with nrot_ vs. nrot, as the former is 1 but the
latter is 48 before the call to find_sym in setup.f90 line 513, but
find_sym internally uses nrot.
cheers
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 <mailto: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
> <mailto: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 <mailto: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@ <mailto: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
>
>
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--
Lorenzo Paulatto - Paris
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