[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??
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Apr 18 11:01:17 CEST 2019
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 <natalie at 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:
> 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
>>
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--
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
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