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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: Mon, 25 Sep 2017 14:00:58 -0400

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
>
>
>
>
>
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-- 
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.