Thanks! Then it is not likely that a Ga-N bond can reach 2.5 A if its
equilibrium value is 2.05 A. If this happens, I would expect the dynamics
is badly described by the potential. The Tersoff cutoff function is very
problematic.
Before you give up, I suggest you use a longer correlation time.
First, you can change line 19 in the file ex4/ballistic/plot_shc.m from
Nc = 250;
to
Nc = 500;
This will use the full correlation time as in you run.in file (1 ps).
If this does not help much, also try to change
compute_shc 2 500 10000 5 6
to
compute_shc 5 500 10000 5 6
Then, you need to change
dt=2; %fs
in line 5 of ex4/ballistic/plot_shc.m to
dt=5; %fs
The reason for these changes is that I guess your GaN system has some
long-time dynamics.
Good luck!
Zheyong
On Thu, Nov 7, 2019 at 8:57 AM Mostafa Valadkhani <mostafa.v68@xxxxxxxxx>
wrote:
Dear Zheyong
I'm really looking forward for GKMA implementation in GPUMD. I asked Alex
and he told me, he is working on that very actively, hope I can use it soon.
GaN and AlN structures are monolayer hexagonal lattice like Graphene you
can find the GaN xyz as attached and in this paper
<https://pubs.rsc.org/en/content/articlelanding/2017/nr/c7nr01271c#!divAbstract>,
so there is no Ga-Ga and N-N bondings.
About the second Qs, if I get it correctly, bond length of Al-N is 1.97
and R1,R2 are 2.4,2.7 but in Ga-N bond length is about 2.05 and R1,R2 are
2.5 and 2.8 respectively.
Thanks,
M. V.
________________
Mostafa Valadkhani
Department of Mechanical Engineering,
University of Tehran,
Tehran, Iran
mostafa.v68@xxxxxxxxx | valadkhani.m@xxxxxxxx
On Wed, Nov 6, 2019 at 9:39 AM FreeLists Mailing List Manager <
ecartis@xxxxxxxxxxxxx> wrote:
gpumd Digest Tue, 05 Nov 2019 Volume: 01 Issue: 026
In This Issue:
[gpumd] Re: noises on SHC calculation GaN with GPUMD
[gpumd] Re: noises on SHC calculation GaN with GPUMD
[gpumd] The factor 160 in thermal conductance term on
plot_s
[gpumd]
=?GBK?B?UmU6W2dwdW1kXSBUaGUgZmFjdG9yIDE2MCBpbiB0aGVy
[gpumd] Re: The factor 160 in thermal conductance term
----------------------------------------------------------------------
From: Bruce Fan <brucenju@xxxxxxxxx>
Date: Tue, 5 Nov 2019 09:33:44 +0200
Subject: [gpumd] Re: noises on SHC calculation GaN with GPUMD
Dear Mostafa,
I (and others) also noticed that the spectral heat current (SHC) method as
implemented in GPUMD might give weird results for some systems. The exact
reason for the failure of this method for some systems is not entirely
clear to me, but it is not likely due to a hidden bug is the code, but due
to the applicability of the method as implemented in GPUMD. This method
was
proposed by Saaskilahti et al, and can be traced back to some earlier
works
in Volz's group. It might be the case that the heat current *should be*
calculated from the force constants, up to a given order, say the second
order as in most previous works. In contrast, I have implemented the full
heat current in GPUMD.
Can I ask a few questions on your model and potential?
-- Are there Ga-Ga and N-N bonds in your structure?
-- Are there any bond lengths r within the corresponding two cutoff
distances R1 and R2: R1 < r < R2?
-- The same question for your AlN system.
I mentioned to you that Alex has implemented a new set of spectral
decomposition methods in GPUMD, mostly based on the Green-Kubo modal
analysis (GKMA) method developed in Henry's group. We will document this
method soon.
Zheyong
On Tue, Nov 5, 2019 at 7:29 AM Mostafa Valadkhani <mostafa.v68@xxxxxxxxx>
wrote:
Dear all,to
I'm calculation SHC of AlN and GaN with implementing tersoff potential
GPUMD,became
The results for AlN was reasonable but for GaN I have some sin noises as
attached on the result don't know why! The run.in file is as:
potential potentials/tersoff/NGa.tersoff.txt 0 1
velocity 300
ensemble nvt_ber 300 300 0.01
fix 0
time_step 1
dump_thermo 1000
run 1000000
ensemble heat_lan 300 200 10 1 10
fix 0
dump_position 10000
compute 0 10 1000 temperature
compute_shc 2 500 10000 5 6
run 20000000
I doubled the run time and averaging in compute_shc and the results
even worse.
Any idea to fix the results?
thanks,
M. V.
________________
Mostafa Valadkhani
Department of Mechanical Engineering,
University of Tehran,
Tehran, Iran
mostafa.v68@xxxxxxxxx | valadkhani.m@xxxxxxxx
------------------------------
From: Bruce Fan <brucenju@xxxxxxxxx>
Date: Tue, 5 Nov 2019 09:39:56 +0200
Subject: [gpumd] Re: noises on SHC calculation GaN with GPUMD
Another note:
You can notice from panel (b) of you figure that the total heat current is
about 0.75 eV/ps, which is the same of K(t=0) from panel (c). So the
K(t=0)
value is correct (this is a confirmation of energy conservation), but the
whole K(t) curve is "problematic".
Zheyong
On Tue, Nov 5, 2019 at 9:33 AM Bruce Fan <brucenju@xxxxxxxxx> wrote:
Dear Mostafa,as
I (and others) also noticed that the spectral heat current (SHC) method
implemented in GPUMD might give weird results for some systems. Theexact
reason for the failure of this method for some systems is not entirelydue
clear to me, but it is not likely due to a hidden bug is the code, but
to the applicability of the method as implemented in GPUMD. This methodwas
proposed by Saaskilahti et al, and can be traced back to some earlierworks
in Volz's group. It might be the case that the heat current *should be*full
calculated from the force constants, up to a given order, say the second
order as in most previous works. In contrast, I have implemented the
heat current in GPUMD.mostafa.v68@xxxxxxxxx>
Can I ask a few questions on your model and potential?
-- Are there Ga-Ga and N-N bonds in your structure?
-- Are there any bond lengths r within the corresponding two cutoff
distances R1 and R2: R1 < r < R2?
-- The same question for your AlN system.
I mentioned to you that Alex has implemented a new set of spectral
decomposition methods in GPUMD, mostly based on the Green-Kubo modal
analysis (GKMA) method developed in Henry's group. We will document this
method soon.
Zheyong
On Tue, Nov 5, 2019 at 7:29 AM Mostafa Valadkhani <
wrote:to
Dear all,
I'm calculation SHC of AlN and GaN with implementing tersoff potential
asGPUMD,
The results for AlN was reasonable but for GaN I have some sin noises
attached on the result don't know why! The run.in file is as:
potential potentials/tersoff/NGa.tersoff.txt 0 1
velocity 300
ensemble nvt_ber 300 300 0.01
fix 0
time_step 1
dump_thermo 1000
run 1000000
ensemble heat_lan 300 200 10 1 10
fix 0
dump_position 10000
compute 0 10 1000 temperature
compute_shc 2 500 10000 5 6
run 20000000
I doubled the run time and averaging in compute_shc and the results
became even worse.
Any idea to fix the results?
thanks,
M. V.
________________
Mostafa Valadkhani
Department of Mechanical Engineering,
University of Tehran,
Tehran, Iran
mostafa.v68@xxxxxxxxx | valadkhani.m@xxxxxxxx
------------------------------
From: =?UTF-8?B?IuyGjOyInOyEsSI=?= <soonsung2001@xxxxxxxxxx>
Date: Wed, 6 Nov 2019 11:04:54 +0900
Subject: [gpumd] The factor 160 in thermal conductance term on plot_shc.m
file.
Dear Zheyong.
Thank you to Zheyong Fan for using this good GPUMD program.
Today, I have question.
I looked the plot_shc.m file in example folder (ex4, in the folder named
"ballistic")
and found that there is coefficient 160 in the line which stated about
thermal conductance term.
DT=165.75; (temperature difference)
A=0.142*sqrt(3)*81*0.335; (cross-sectional area) % nm^2
Gic=160*qi/A/DT;
Goc=160*qo/A/DT;
And I have the question here that what is the meaning of factors "160" in
Gicand Goc ??Are they just arbitrary factors?
[IMG]
[IMG]
------------------------------
Date: Wed, 06 Nov 2019 11:12:28 +0800
From: "=?GBK?B?tq26o7/t?=" <dhk@xxxxxxxxxx>
Subject: [gpumd]
=?GBK?B?UmU6W2dwdW1kXSBUaGUgZmFjdG9yIDE2MCBpbiB0aGVybWE=?=
/�þYZ�Ì ¯*.����ب��á{ýz���¶ �ž+\¢{ޮȨ�������ç!jÁ
------------------------------
From: =?UTF-8?B?IuyGjOyInOyEsSI=?= <soonsung2001@xxxxxxxxxx>
Date: Wed, 6 Nov 2019 12:37:28 +0900
Subject: [gpumd] Re: The factor 160 in thermal conductance term
Dear haikuan
Thank you for your kind answer~!
Soonsung So.
--------- 원본 메일 ---------보낸사람 : "董海宽" <dhk@xxxxxxxxxx>
받는사람 : <gpumd@xxxxxxxxxxxxx>
받은날짜 : 2019년 Nov 6일(Wed) 12:12:43
제목 : [gpumd] Re:[gpumd] The factor 160 in thermal conductance term on
plot_shc.m file.
Hi,
I'll answer your question.
The "160" is the unit conversion factor.
such as G=160*Q/A/temp_difference,
where, G (GW/m^2K), Q (eV/ps), A (nm^2), and temp_difference(K) need to
be
unified in units.
For heat flux Q， 1 (ev/ps) = 1.60*10^{-19} /10^{-12} (J/s) = 1.60*10^{-7}
(W).
That should make sense to you.
haikuan
---------- Origin message ----------
From："" <soonsung2001@xxxxxxxxxx>file.
To：gpumd@xxxxxxxxxxxxx
Subject：[gpumd] The factor 160 in thermal conductance term on plot_shc.m
Date：2019-11-06 10:04:54
[IMG]
[IMG]
------------------------------
End of gpumd Digest V1 #26
**************************
