[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 11:58:52 CEST 2019
Oh well. I see: it's an unintended side effect of a bug fix to 6.3, present
in 6.3-backports.
There is a simple solution, not guarantee to be
unintended-side-effect-free, though:
diff --git a/PW/src/setup.f90 b/PW/src/setup.f90
index 0918ac017..135e58789 100644
--- a/PW/src/setup.f90
+++ b/PW/src/setup.f90
@@ -519,7 +519,10 @@ SUBROUTINE setup()
!
! ... nosym: do not use any point-group symmetry (s(:,:,1) is the
identity)
!
- IF ( nosym ) nsym = 1
+ IF ( nosym ) THEN
+ nsym = 1
+ invsym = .FALSE.
+ END IF
!
IF ( nsym > 1 .AND. ibrav == 0 ) CALL infomsg('setup', &
'DEPRECATED: symmetry with ibrav=0, use correct ibrav instead')
Paolo
On Thu, Apr 18, 2019 at 11:11 AM Lorenzo Paulatto <paulatz at gmail.com> wrote:
> > 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
> >
> >
> > _______________________________________________
> > Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso
> )
> > users mailing list users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
> >
>
> --
> Lorenzo Paulatto - Paris
> _______________________________________________
> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at 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
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