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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: Yuka Uemura <ukaron50@...24...>
Date: Tue, 26 Sep 2017 14:56:56 +0900

I am sorry for forgetting to reply to the mailing list and let me resend the below.
Thanks.

Yuka  


2017-09-26 14:32 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:
please always reply to the mailing list and not only to individual
people. thanks, axel.

On Tue, Sep 26, 2017 at 1:28 AM, Yuka Uemura <ukaron50@...24...> wrote:
> Axel
>
> Thank you very much for your reply and I am sorry for not explaining enough.
>
>>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
>
> 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.
>
> 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@...655....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.