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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.

**Follow-Ups**:**Re: [lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result***From:*Yuka Uemura <ukaron50@...24...>

**References**:**[lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result***From:*Yuka Uemura <ukaron50@...24...>

**Re: [lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result***From:*Axel Kohlmeyer <akohlmey@...24...>

**Re: [lammps-users] the region temperature calculated by <compute temp/region> command shows invalid result***From:*Yuka Uemura <ukaron50@...24...>

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