subject:"\[QE\-users\] Change in temperature control for md simulation in QE 6.4.1 compared with 6.3"

Re: [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??

2019-04-18 Thread Holzwarth, Natalie

Dear Paolo and Lorrenzo,
Thanks so much for your analysis of this issue. The patch to setup.f90
in the 6.4.1 release does seem to fix this problem at least for the simple
NaCl supercell. Thanks again.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 Thu, Apr 18, 2019 at 5:59 AM Paolo Giannozzi 
wrote:

> 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 
> 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:
>> > 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 > > > 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   6.3QE 6.4.1
>> >   temperature=  1800. K   temperature=
>> >   0. K
>> >   temperature=  1798.79298998 K   temperature=
>> >   0. K
>> >   temperature=  1795.18924725 K   temperature=
>> >   0.0001 K
>> >   temperature=  1789.20477087 K   temperature=
>> >   0.0002 K
>> >   temperature=  1780.85173941 K   temperature=
>> >   0.0048 K
>> >   temperature=  1770.15802096 K   temperature=
>> >   0.0014 K
>> >   temperature=  1757.15885289 K   temperature=
>> >   0.0032 K
>> >   temperature=  1741.89911601 K   temperature=
>> >   0.0575 K
>> >   temperature=  1724.42918183 K   temperature=
>> >   0.1204 K
>> >   temperature=  1704.80836203 K   temperature=
>> >   0.1108 K
>> >   temperature=  1683.10589232 K   temperature=
>> >   0.0872 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
>>

Re: [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??

2019-04-18 Thread Paolo Giannozzi

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  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:
> > 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  > > 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   6.3QE 6.4.1
> >   temperature=  1800. K   temperature=
> >   0. K
> >   temperature=  1798.79298998 K   temperature=
> >   0. K
> >   temperature=  1795.18924725 K   temperature=
> >   0.0001 K
> >   temperature=  1789.20477087 K   temperature=
> >   0.0002 K
> >   temperature=  1780.85173941 K   temperature=
> >   0.0048 K
> >   temperature=  1770.15802096 K   temperature=
> >   0.0014 K
> >   temperature=  1757.15885289 K   temperature=
> >   0.0032 K
> >   temperature=  1741.89911601 K   temperature=
> >   0.0575 K
> >   temperature=  1724.42918183 K   temperature=
> >   0.1204 K
> >   temperature=  1704.80836203 K   temperature=
> >   0.1108 K
> >   temperature=  1683.10589232 K   temperature=
> >   0.0872 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

Re: [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??

2019-04-18 Thread Lorenzo Paulatto

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: 
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 > 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. K       temperature    =   
  0. K
      temperature    =  1798.79298998 K       temperature    =   
  0. K
      temperature    =  1795.18924725 K       temperature    =   
  0.0001 K
      temperature    =  1789.20477087 K       temperature    =   
  0.0002 K
      temperature    =  1780.85173941 K       temperature    =   
  0.0048 K
      temperature    =  1770.15802096 K       temperature    =   
  0.0014 K
      temperature    =  1757.15885289 K       temperature    =   
  0.0032 K
      temperature    =  1741.89911601 K       temperature    =   
  0.0575 K
      temperature    =  1724.42918183 K       temperature    =   
  0.1204 K
      temperature    =  1704.80836203 K       temperature    =   
  0.1108 K
      temperature    =  1683.10589232 K       temperature    =   
  0.0872 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


   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.,
/

   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

Re: [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??

2019-04-18 Thread Paolo Giannozzi

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  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 
> 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   6.3QE 6.4.1
>>  temperature=  1800. K   temperature=
>>  0. K
>>  temperature=  1798.79298998 K   temperature=
>>  0. K
>>  temperature=  1795.18924725 K   temperature=
>>  0.0001 K
>>  temperature=  1789.20477087 K   temperature=
>>  0.0002 K
>>  temperature=  1780.85173941 K   temperature=
>>  0.0048 K
>>  temperature=  1770.15802096 K   temperature=
>>  0.0014 K
>>  temperature=  1757.15885289 K   temperature=
>>  0.0032 K
>>  temperature=  1741.89911601 K   temperature=
>>  0.0575 K
>>  temperature=  1724.42918183 K   temperature=
>>  0.1204 K
>>  temperature=  1704.80836203 K   temperature=
>>  0.1108 K
>>  temperature=  1683.10589232 K   temperature=
>>  0.0872 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 ${SLURM_SUBMIT_DIR}
>>
>> cat > NaCl.in << EOF
>>
>> 
>>   calculation = "md",
>>   pseudo_dir  =
>> '/deac/natalieGrp/wfurc9/natalie/EL6/rc9/PAWatoms/poscorenhat/',
>>   verbosity   = "high",
>>   outdir  = "$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.,
>> /
>> 
>>   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,
>> /
>> 
>>   conv_thr= 1.D-8,
>>   electron_maxstep = 200,
>> /
>> 
>>

Re: [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??

2019-04-17 Thread 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:
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  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   6.3QE 6.4.1
>  temperature=  1800. K   temperature=
>  0. K
>  temperature=  1798.79298998 K   temperature=
>  0. K
>  temperature=  1795.18924725 K   temperature=
>  0.0001 K
>  temperature=  1789.20477087 K   temperature=
>  0.0002 K
>  temperature=  1780.85173941 K   temperature=
>  0.0048 K
>  temperature=  1770.15802096 K   temperature=
>  0.0014 K
>  temperature=  1757.15885289 K   temperature=
>  0.0032 K
>  temperature=  1741.89911601 K   temperature=
>  0.0575 K
>  temperature=  1724.42918183 K   temperature=
>  0.1204 K
>  temperature=  1704.80836203 K   temperature=
>  0.1108 K
>  temperature=  1683.10589232 K   temperature=
>  0.0872 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 ${SLURM_SUBMIT_DIR}
>
> cat > NaCl.in << EOF
>
> 
>   calculation = "md",
>   pseudo_dir  =
> '/deac/natalieGrp/wfurc9/natalie/EL6/rc9/PAWatoms/poscorenhat/',
>   verbosity   = "high",
>   outdir  = "$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.,
> /
> 
>   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,
> /
> 
>   conv_thr= 1.D-8,
>   electron_maxstep = 200,
> /
> 
>  ion_dynamics = 'verlet',
>  ion_temperature = 'initial',
>  tempw = 1800.d0,
>  pot_extrapolation = 'second-order',
>  wfc_extrapolation = 'second-order',
> /
> 
>   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   0.0  0.0  0.0
> Na   0.5  0.5  0.0
> Na   0.0  0.5  0.5
> Na   0.5  0.0  0.5
> Cl

[QE-users] Change in temperature control for md simulation in QE 6.4.1 compared with 6.3

2019-04-10 Thread Holzwarth, Natalie

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   6.3QE 6.4.1
 temperature=  1800. K   temperature=
 0. K
 temperature=  1798.79298998 K   temperature=
 0. K
 temperature=  1795.18924725 K   temperature=
 0.0001 K
 temperature=  1789.20477087 K   temperature=
 0.0002 K
 temperature=  1780.85173941 K   temperature=
 0.0048 K
 temperature=  1770.15802096 K   temperature=
 0.0014 K
 temperature=  1757.15885289 K   temperature=
 0.0032 K
 temperature=  1741.89911601 K   temperature=
 0.0575 K
 temperature=  1724.42918183 K   temperature=
 0.1204 K
 temperature=  1704.80836203 K   temperature=
 0.1108 K
 temperature=  1683.10589232 K   temperature=
 0.0872 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


  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.,
/

  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,
/

  conv_thr= 1.D-8,
  electron_maxstep = 200,
/

 ion_dynamics = 'verlet',
 ion_temperature = 'initial',
 tempw = 1800.d0,
 pot_extrapolation = 'second-order',
 wfc_extrapolation = 'second-order',
/

  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   0.0  0.0  0.0
Na   0.5  0.5  0.0
Na   0.0  0.5  0.5
Na   0.5  0.0  0.5
Cl   0.5  0.5  0.5
Cl   0.0  0.0  0.5
Cl   0.5  0.0  0.0
Cl   0.0  0.5  0.0
K_POINTS AUTOMATIC
2 2 2 1 1 1
EOF

mpirun $PW  -in  NaCl.in  >  NaCl.out

-

N. A. W. Holzwarth   email: natalie@

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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Re: [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??

Re: [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??

Re: [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??

Re: [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??

Re: [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??

[QE-users] Change in temperature control for md simulation in QE 6.4.1 compared with 6.3

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