[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

From: |
Yuka Uemura <ukaron50@...24...> |

Date: |
Tue, 26 Sep 2017 23:01:30 +0900 |

Dr. Axel Kohlmeyer

I will check whether the atoms are existed inside each regions during the simulation.

Yuka Uemura

2017-09-26 20:30 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:

On Tue, Sep 26, 2017 at 1:56 AM, Yuka Uemura <ukaron50@...29....> 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@...396...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@...43...4... http://goo.gl/1wk0

College of Science & Technology, Temple University, Philadelphia PA, USA

International Centre for Theoretical Physics, Trieste. Italy.

**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...>

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

- Prev by Date:
**Re: [lammps-users] Compilation warning** - Next by Date:
**[lammps-users] ERROR: No pair reax/c for fix qeq/reax** - Previous by thread:
- Next by thread:
**[lammps-users] How to use molecular's quaternions for orientation-dependent forces calculation with "hybrid sphere molecular" style?** - Index(es):