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Re: [lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result
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Re: [lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 26 Sep 2017 07:30:39 -0400

On Tue, Sep 26, 2017 at 1:56 AM, Yuka Uemura <ukaron50@...24...> wrote:

[...]

>> >>have you checked, whether are are actually atoms inside those regions?
>> > yes, I have set the 5nm x 5nm square flake and the result of log file,
>> > the number of each region of flake "n" to divide n1 to n5 is as follows;
>> >
>> > group n1 region n1
>> > 176 atoms in group n1
>> > group n2 region n2
>> > 176 atoms in group n2
>> > group n3 region n3
>> > 176 atoms in group n3
>> > group n4 region n4
>> > 176 atoms in group n4
>> > group n5 region n5
>> > 198 atoms in group n5
>> >

this is no proof at all. this shows that there were atoms in your
regions _at the beginning_ of your simulation.
it doesn't say anything about how many atoms are in those regions
_during_ the simulation.

>> > And the temperature of each region of flake is apt to show higher
>> > temperature(700 to 1000K) for a moment just before they show 0 Kelvin.

which is still in full accordance with your system building a
significant center of mass drift and thus moving out of the reach of
the measuring regions.

you need to provide more convincing information to prove that there is
not a problem with your setup but with LAMMPS.

axel.

>> >
>> > thank you very much for your help in advance.
>> >
>> > Yuka
>> >
>> >
>> >
>> > 2017-09-26 3:00 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:
>> >>
>> >> On Sat, Sep 23, 2017 at 3:14 AM, Yuka Uemura <ukaron50@...24...>
>> >> wrote:
>> >> > Dear Sir,
>> >> >
>> >> > [Problem]
>> >> > Although the individual atoms have kinetic energy, the region
>> >> > temperature
>> >> > calculated by <compute temp/region> command shows 0 Kelvin.
>> >> > Such results are hard to think actually and I would like to teach
>> >> > improvement if it is a software bug or setting problem.
>> >>
>> >> please note, that posting excel spreadsheets is pointless. to most
>> >> people they don't make no sense without suitable explanations.
>> >>
>> >> >
>> >> > The outline of the simulation and the result are as follows;
>> >> > · Investigate the moving behavior of flake when flake is placed on a
>> >> > substrate with a temperature gradient
>> >> > · Dividing the flake n to calculate the average temperature for each
>> >> > region
>> >> > (n1 to n5)
>> >> > · Although the distribution of kinetic energy is almost unchanged at
>> >> > each
>> >> > time step,
>> >> >   the average temperature for each is different
>> >> > the average temperature of 33000 steps:  (n1,n2,n3,n4,n5)=(295, 265,
>> >> > 261,
>> >> > 237, 245)
>> >> > the average temperature of 300000 steps:(n1,n2,n3,n4,n5)=(0, 0, 0, 0,
>> >> > 274)
>> >> >
>> >> > attached file are raw data of the atoms of flake and  k line shows
>> >> > the
>> >> > kinetic energy.
>> >>
>> >> have you checked, whether are are actually atoms inside those regions?
>> >>
>> >> axel.
>> >>
>> >>
>> >> >
>> >> > regards,
>> >> >>
>> >> >> Yuka Uemura
>> >> >> Department of Mechanical Engineering and Intelligent Systems,
>> >> >> The University of Electro-Communications
>> >> >
>> >> >
>> >> > relating script is below;
>> >> >
>> >> > units metal
>> >> > boundary f p f
>> >> > atom_style      atomic
>> >> > lattice sc 1
>> >> > read_data
>> >> > mass
>> >> >
>> >> > pair_style  airebo 3.0
>> >> > pair_coeff * *
>> >> >
>> >> > neighbor 0.3 nsq
>> >> > neigh_modify delay 1
>> >> >
>> >> > region n block INF INF INF INF 29 INF
>> >> > #cubic
>> >> > region n1 block INF -159 INF INF 29 INF
>> >> > region n2 block -159 -153 INF INF 29 INF
>> >> > region n3 block -153 -147 INF INF 29 INF
>> >> > region n4 block -147 -141 INF INF 29 INF
>> >> > region n5 block -141 INF INF INF 29 INF
>> >> >
>> >> > group n region n
>> >> > group n1 region n1
>> >> > group n2 region n2
>> >> > group n3 region n3
>> >> > group n4 region n4
>> >> > group n5 region n5
>> >> >
>> >> > compute comn n com
>> >> >
>> >> > compute pall all pe/atom
>> >> > compute kall all ke/atom
>> >> >
>> >> > compute pe all pe
>> >> > compute pflake all reduce/region n sum c_pall
>> >> > compute ke all ke
>> >> >
>> >> >
>> >> > compute tn all temp/region n
>> >> > compute t_n1 all temp/region n1
>> >> > compute t_n2 all temp/region n2
>> >> > compute t_n3 all temp/region n3
>> >> > compute t_n4 all temp/region n4
>> >> > compute t_n5 all temp/region n5
>> >> >
>> >> > compute stress all stress/atom
>> >> >
>> >> > variable stress_xx atom c_stress[1]
>> >> > variable stress_yy atom c_stress[2]
>> >> > variable stress_zz atom c_stress[3]
>> >> >
>> >> > thermo 100
>> >> > thermo_style custom step etotal pe ke c_tall c_tb c_tc c_td c_te c_tf
>> >> > c_tg
>> >> > c_th c_ti c_tj c_tk
>> >> > thermo_modify temp tall
>> >> >
>> >> > #minimize 0.0 1.0e-6 100 500000
>> >> > #reset_timestep  0
>> >> >
>> >> > timestep 0.001
>> >> >
>> >> > fix nvtb b nvt temp 300 300 0.1
>> >> > fix nvtk k nvt temp 200 200 0.1
>> >> > fix nve free nve
>> >> >
>> >> > velocity all create 1 581277 temp tall
>> >> >
>> >> > velocity a set 0 0 0
>> >> > velocity l set 0 0 0
>> >> > velocity n set 0 0 0
>> >> >
>> >> > fix fa a setforce 0 0 0
>> >> > fix fl l setforce 0 0 0
>> >> >
>> >> > fix fn n setforce 0 0 0
>> >> >
>> >> > dump 2 n cfg 1000 n.*.cfg id type xs ys zs vx vy vz x y z c_pall
>> >> > c_kall
>> >> > v_stress_xx v_stress_yy v_stress_zz id
>> >> > dump 3 all cfg 1000 graphene.*.cfg id type xs ys zs vx vy vz x y z
>> >> > c_pall
>> >> > c_kall v_stress_xx v_stress_yy v_stress_zz id
>> >> >
>> >> > fix data all ave/time 1 1000 1000 c_pe c_ke c_tall c_pflake file
>> >> > data.dat
>> >> >
>> >> > fix temp all ave/time 1 100 100 c_tb c_tc c_td c_te c_tf c_tg c_th
>> >> > c_ti
>> >> > c_tj
>> >> > c_tk c_tn file temp.dat
>> >> > fix temp_cubic all ave/time 1 100 100 c_t_n1 c_t_n2 c_t_n3 c_t_n4
>> >> > c_t_n5
>> >> > file temp_cubic.dat
>> >> >
>> >> > unfix                       fn
>> >> >
>> >> > run 5000000
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Check out the vibrant tech community on one of the world's most
>> >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> >> > _______________________________________________
>> >> > lammps-users mailing list
>> >> > lammps-users@lists.sourceforge.net
>> >> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> >> College of Science & Technology, Temple University, Philadelphia PA,
>> >> USA
>> >> International Centre for Theoretical Physics, Trieste. Italy.
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.