Re: [lammps-users] questions on tmp.profile

On Tue, Jun 8, 2010 at 11:19 AM, Matt K. Petersen <matt@hec.utah.edu> wrote:

It looks to me like you need to sample longer, and/or swap more
frequently. Don't use fewer bins.
Matt

Quoting "JhonY. I." <yijhon@hotmail.com>:

>
> I've got temperature profile to get thermal conducitivity using
> "thermal conductivity using fix" and "thermal/conductivity and fix
> ave/spatial" commands.
>
> The result is as follows.
>
> 101000 25
> 1 -0.7175 0 0
> 2 0.7175 23.69 291.21
> 3 2.1525 24.31 299.481
> 4 3.5875 16 315.053
> 5 5.0225 16 303.967
> 6 6.4575 16 298.175
> 7 7.8925 16 308.913
> 8 9.3275 23.84 281.964
> 9 10.7625 24.16 281.042
> 10 12.1975 16 290.864
> 11 13.6325 16 307.152
> 12 15.0675 16 309.009
> 13 16.5025 16 304.191
> 14 17.9375 23.35 339.291
> 15 19.3725 24.65 311.915
> 16 20.8075 16 313.163
> 17 22.2425 16 304.582
> 18 23.6775 16 300.64
> 19 25.1125 16 282.925
> 20 26.5475 23.56 280.165
> 21 27.9825 24.44 292.552
> 22 29.4175 16 298.56
> 23 30.8525 16 295.138
> 24 32.2875 16 289.97
> 25 33.7225 16 271.865
> ...
>
> The direction of thrmal propation is z axis.
> The z length was 34.439999 A and I determine delta of "fix
> ave/spatial command" as 34.439999/24 ~ 1.435 A since I use 24 bins
> in "fix thermal/conducitivity command".
>
>
> I think the first 1 layer of the result is the same with 25 layer
> (34.439999 - 0.7175 ~ 33.7225)
>
> and the 1 layer may be ignored. (It should appear by a certain bug
> of LAMMPS, I guess)
>
>
> The result does not show monotonous trend but exhibit. somewhat rugged form.
> Thus, I increase the delta two times (2.87 A) and change swap number
> from 1 to 2 and the corresponding result is
>
> as follows.
>
>
> 101000 13
> 1 -1.435 0 0
> 2 1.435 48 304.582
> 3 4.305 32 299.893
> 4 7.175 32 296.51
> 5 10.045 48 279.546
> 6 12.915 32 303.297
> 7 15.785 32 314.86
> 8 18.655 48 346.408
> 9 21.525 32 320.751
> 10 24.395 32 288.373
> 11 27.265 48 279.248
> 12 30.135 32 292.802
> 13 33.005 32 261.722
>
>
>
> It still does not show monotonous linear form.
>
> In spite of it, Is it all right? May I take dT/dz as
> (346.408-261.722)/(33.005-18.655).
>
>
> Otherwise, should I have more monotonous result and should it has
> more linear shape?
> If so, what points should I check in running the simulation to get
> such a result?
>
>
>
> Is it common to determine delta to be length/(number of bins of
> "fix themal/conducitivity command") as such in my first try?
> Otherwise, should it be multiple of it or so generally?
>
>
>
>
> Cheers,
>
>
>
> Luke
>
>
>
> _________________________________________________________________
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________________________________________________
Dr. Matt K. Petersen,
Center for Biophysical Modeling and Simulation
and Department of Chemistry,
University of Utah
________________________________________________

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From:	"JhonY. I." <yijhon@hotmail.com>
Date:	Sat, 12 Jun 2010 15:35:15 +0000