Yes, "lj 2" should be in the first line of the LJ potential file.
Could you ask the other question in a different thread with a good title?
Within this thread, it's better to focus on your original question related
to
double-layer graphene simulation.
Zheyong
On Thu, Oct 17, 2019 at 9:22 AM Mostafa Valadkhani <mostafa.v68@xxxxxxxxx>
wrote:
Thanks for the comments
Do I have to keep "lj 2" at the first line?
lj 2 (or even lj 4?)
2.84e-3 3.405 0
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
2.84e-3 3.405 0
I have another problem with the potential command, assume I implement
SiCGe.tersoff to the GPUMD potentials and the parameters are set as you
said in the manual:
000
001
...
120
121
122
200
201
210
...
220
221
222
how I'm suppose to define which atom type is Ge or C or Si?
in lammps easily we define like "pair_coeff * * SiC.tersoff Si C Si"
and how it is possible to use this potential for a system with only two
atom types with only Si and C for example?
Cheers,
Mostafa
On Thu, Oct 17, 2019 at 8:38 AM FreeLists Mailing List Manager <
ecartis@xxxxxxxxxxxxx> wrote:
gpumd Digest Wed, 16 Oct 2019 Volume: 01 Issue: 023
In This Issue:
[gpumd]
[gpumd] Re: [gpumd]
[gpumd] Re: [gpumd]
[gpumd] CUDA Error on GPUMD
[gpumd] Re: [gpumd]
[gpumd] Re: [gpumd]
[gpumd] Re: [gpumd]
[gpumd] problems with phonon - Vashista
----------------------------------------------------------------------
From: Mostafa Valadkhani <mostafa.v68@xxxxxxxxx>
Date: Wed, 16 Oct 2019 17:11:45 +0330
Subject: [gpumd]
Hi
Sorry if I ask a lot and time to time. Actually I'm calculating SHC with
lammps using Kimmo Codes and wanna relate it somehow with the results
from
GPUMD.
I wanna calculate SHC on the bilayer/monolayer graphene as your paper
with
Ali.The attachments are my inputs, when I run the script following error
comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on GPUMD too.
Thanks,
M.V.
------------------------------
From: Bruce Fan <brucenju@xxxxxxxxx>
Date: Wed, 16 Oct 2019 16:58:00 +0300
Subject: [gpumd] Re: [gpumd]
Hi Mostafa,
So the simulation was done using a developing version, right?
First, I add the contents of your LJ potential file here (you sent me
this
in a private email):
lj 1
2.84e-3 3.405 10.0
Will this contradict the line
potential potentials/lj/c_clj.txt 0 1
in the run.in file?
@Alex Gabourie <gabourie@xxxxxxxxxxxx> How do you think?
Apart from this, I notice a possible source of error in the first line of
xyz.in:
17466 50 11 0 0 1
Here, the parameter M (maximum number of neighbors) is set to 50. This
seems to be too small for a cutoff of 10 Angstrom (from the LJ part). You
can change it to 500. This might be the reason for the error message you
got.
Best,
Zheyong
On Wed, Oct 16, 2019 at 4:42 PM Mostafa Valadkhani <
mostafa.v68@xxxxxxxxx>
wrote:
Hiwith
Sorry if I ask a lot and time to time. Actually I'm calculating SHC
lammps using Kimmo Codes and wanna relate it somehow with the resultsfrom
GPUMD.with
I wanna calculate SHC on the bilayer/monolayer graphene as your paper
Ali.The attachments are my inputs, when I run the script followingerror
comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on GPUMD too.
Thanks,
M.V.
------------------------------
Subject: [gpumd] Re: [gpumd]
From: Alex Gabourie <agabourie47@xxxxxxxxx>
Date: Wed, 16 Oct 2019 10:24:52 -0700
Mostafa,
It's tough to say exactly what might cause that problem, but I think
that Zheyong is correct in that the LJ potential definition is
incorrect. Since you have two atom types defined, the LJ potential must
be of the form 'lj 2'. The fix is simple. Your lj file can look like:
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
Zheyong is also right in that you'll need to increase your neighborlist
size but, if that doesn't work, make sure that you are building GPUMD
with the -DDEBUG flag removed in the makefile. I've had that cause me
memory problems before.
Regards,
Alex
On 10/16/19 6:58 AM, Bruce Fan wrote:
Hi Mostafa,too.
So the simulation was done using a developing version, right?
First, I add the contents of your LJ potential file here (you sent me
this in a private email):
lj 1
2.84e-3 3.405 10.0
Will this contradict the line
potential potentials/lj/c_clj.txt 0 1
in the run.in <http://run.in> file?
@Alex Gabourie <mailto:gabourie@xxxxxxxxxxxx> How do you think?
Apart from this, I notice a possible source of error in the first line
of xyz.in <http://xyz.in>:
17466 50 11 0 0 1
Here, the parameter M (maximum number of neighbors) is set to 50. This
seems to be too small for a cutoff of 10 Angstrom (from the LJ part).
You can change it to 500. This might be the reason for the error
message you got.
Best,
Zheyong
On Wed, Oct 16, 2019 at 4:42 PM Mostafa Valadkhani
<mostafa.v68@xxxxxxxxx <mailto:mostafa.v68@xxxxxxxxx>> wrote:
Hi
Sorry if I ask a lot and time to time. Actually I'm calculating
SHC with lammps using Kimmo Codes and wanna relate it somehow with
the results from GPUMD.
I wanna calculate SHC on the bilayer/monolayer graphene as your
paper with Ali.The attachments are my inputs, when I run the
script following error comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on GPUMD
Thanks,
M.V.
------------------------------
From: Mostafa Valadkhani <mostafa.v68@xxxxxxxxx>
Date: Wed, 16 Oct 2019 21:56:21 +0330
Subject: [gpumd] CUDA Error on GPUMD
Hi
I want to calculate SHC just like ballistic one in examples, I have two
graphene layer with lenard jones interaction between, and my run.in
script
is as :
potential_definition type
potential potentials/tersoff/Graphene_Lindsay_2010_modified.txt 0
potential potentials/tersoff/Graphene_Lindsay_2010_modified.txt 1
potential potentials/lj/c_clj.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 30 11 10
fix 0
dump_position 10000
compute 0 10 1000 temperature
compute_shc 2 250 10000 7 8
run 10000000
and my xyz.in as :
17466 50 11 0 0 1
1 1 0 101.6876192 305.04016 6.75
0 1.2403002 0.0 0.0 12.0 0
0 0.0 0.71609 0.0 12.0 0
0 0.0 2.14827 0.0 12.0 0
...
when I run the script it ends up with the following error :
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
any hint? or help?
thanks
M. V.
------------------------------
From: Bruce Fan <brucenju@xxxxxxxxx>
Date: Wed, 16 Oct 2019 21:31:01 +0300
Subject: [gpumd] Re: [gpumd]
Alex,
should this
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
be changed to
2.84e-3 3.405 0
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
2.84e-3 3.405 0
for his problem?
It means that intra-layer LJ is excluded. He is simulating double-layer
graphene.
Zheyong
On Wed, Oct 16, 2019 at 8:24 PM Alex Gabourie <agabourie47@xxxxxxxxx>
wrote:
Mostafa,that
It's tough to say exactly what might cause that problem, but I think
Zheyong is correct in that the LJ potential definition is incorrect.Since
you have two atom types defined, the LJ potential must be of the form'lj
2'. The fix is simple. Your lj file can look like:with
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
Zheyong is also right in that you'll need to increase your neighborlist
size but, if that doesn't work, make sure that you are building GPUMD
the -DDEBUG flag removed in the makefile. I've had that cause me memorythis
problems before.
Regards,
Alex
On 10/16/19 6:58 AM, Bruce Fan wrote:
Hi Mostafa,
So the simulation was done using a developing version, right?
First, I add the contents of your LJ potential file here (you sent me
in a private email):of
lj 1
2.84e-3 3.405 10.0
Will this contradict the line
potential potentials/lj/c_clj.txt 0 1
in the run.in file?
@Alex Gabourie <gabourie@xxxxxxxxxxxx> How do you think?
Apart from this, I notice a possible source of error in the first line
xyz.in:You
17466 50 11 0 0 1
Here, the parameter M (maximum number of neighbors) is set to 50. This
seems to be too small for a cutoff of 10 Angstrom (from the LJ part).
can change it to 500. This might be the reason for the error messageyou
got.mostafa.v68@xxxxxxxxx>
Best,
Zheyong
On Wed, Oct 16, 2019 at 4:42 PM Mostafa Valadkhani <
wrote:with
Hi
Sorry if I ask a lot and time to time. Actually I'm calculating SHC
fromlammps using Kimmo Codes and wanna relate it somehow with the results
followingGPUMD.
I wanna calculate SHC on the bilayer/monolayer graphene as your paper
with Ali.The attachments are my inputs, when I run the script
error comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on GPUMD too.
Thanks,
M.V.
------------------------------
Subject: [gpumd] Re: [gpumd]
From: Alex Gabourie <agabourie47@xxxxxxxxx>
Date: Wed, 16 Oct 2019 11:36:28 -0700
Zheyong,
Oh shoot! You are right! Two types requires four entries. To exclude the
intra-layer LJ interactions, the first and last entry in the LJ file
should definitely have a cutoff of 0.
Thank you for correcting me,
Alex
On 10/16/19 11:31 AM, Bruce Fan wrote:
Alex,
should this
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
be changed to
2.84e-3 3.405 0
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
2.84e-3 3.405 0
for his problem?
It means that intra-layer LJ is excluded. He is simulating
double-layer graphene.
Zheyong
On Wed, Oct 16, 2019 at 8:24 PM Alex Gabourie <agabourie47@xxxxxxxxx
<mailto:agabourie47@xxxxxxxxx>> wrote:
Mostafa,
It's tough to say exactly what might cause that problem, but I
think that Zheyong is correct in that the LJ potential definition
is incorrect. Since you have two atom types defined, the LJ
potential must be of the form 'lj 2'. The fix is simple. Your lj
file can look like:
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
Zheyong is also right in that you'll need to increase your
neighborlist size but, if that doesn't work, make sure that you
are building GPUMD with the -DDEBUG flag removed in the makefile.
I've had that cause me memory problems before.
Regards,
Alex
On 10/16/19 6:58 AM, Bruce Fan wrote:
Hi Mostafa,
So the simulation was done using a developing version, right?
First, I add the contents of your LJ potential file here (you
sent me this in a private email):
lj 1
2.84e-3 3.405 10.0
Will this contradict the line
potential potentials/lj/c_clj.txt 0 1
in the run.in <http://run.in> file?
@Alex Gabourie <mailto:gabourie@xxxxxxxxxxxx> How do you think?
Apart from this, I notice a possible source of error in the first
line of xyz.in <http://xyz.in>:
17466 50 11 0 0 1
Here, the parameter M (maximum number of neighbors) is set to 50.
This seems to be too small for a cutoff of 10 Angstrom (from the
LJ part). You can change it to 500. This might be the reason for
the error message you got.
Best,
Zheyong
On Wed, Oct 16, 2019 at 4:42 PM Mostafa Valadkhani
<mostafa.v68@xxxxxxxxx <mailto:mostafa.v68@xxxxxxxxx>> wrote:
Hi
Sorry if I ask a lot and time to time. Actually I'm
calculating SHC with lammps using Kimmo Codes and wanna
relate it somehow with the results from GPUMD.
I wanna calculate SHC on the bilayer/monolayer graphene as
your paper with Ali.The attachments are my inputs, when I run
the script following error comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on
GPUMD too.
Thanks,
M.V.
------------------------------
From: Bruce Fan <brucenju@xxxxxxxxx>
Date: Wed, 16 Oct 2019 21:41:20 +0300
Subject: [gpumd] Re: [gpumd]
Alex,
I though you have changed the grammar :-)
I have not tested multiple potentials after you have changed the keywords
related to the setting up of potentials. Allowing for defining the same
potential twice looks very powerful!
Zheyong
On Wed, Oct 16, 2019 at 9:36 PM Alex Gabourie <agabourie47@xxxxxxxxx>
wrote:
Zheyong,the
Oh shoot! You are right! Two types requires four entries. To exclude
intra-layer LJ interactions, the first and last entry in the LJ fileshould
definitely have a cutoff of 0.that
Thank you for correcting me,
Alex
On 10/16/19 11:31 AM, Bruce Fan wrote:
Alex,
should this
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
be changed to
2.84e-3 3.405 0
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
2.84e-3 3.405 0
for his problem?
It means that intra-layer LJ is excluded. He is simulating double-layer
graphene.
Zheyong
On Wed, Oct 16, 2019 at 8:24 PM Alex Gabourie <agabourie47@xxxxxxxxx>
wrote:
Mostafa,
It's tough to say exactly what might cause that problem, but I think
SinceZheyong is correct in that the LJ potential definition is incorrect.
'ljyou have two atom types defined, the LJ potential must be of the form
neighborlist2'. The fix is simple. Your lj file can look like:
lj 2
2.84e-3 3.405 10.0
2.84e-3 3.405 10.0
Zheyong is also right in that you'll need to increase your
withsize but, if that doesn't work, make sure that you are building GPUMD
memorythe -DDEBUG flag removed in the makefile. I've had that cause me
line ofproblems before.
Regards,
Alex
On 10/16/19 6:58 AM, Bruce Fan wrote:
Hi Mostafa,
So the simulation was done using a developing version, right?
First, I add the contents of your LJ potential file here (you sent me
this in a private email):
lj 1
2.84e-3 3.405 10.0
Will this contradict the line
potential potentials/lj/c_clj.txt 0 1
in the run.in file?
@Alex Gabourie <gabourie@xxxxxxxxxxxx> How do you think?
Apart from this, I notice a possible source of error in the first
Youxyz.in:
17466 50 11 0 0 1
Here, the parameter M (maximum number of neighbors) is set to 50. This
seems to be too small for a cutoff of 10 Angstrom (from the LJ part).
youcan change it to 500. This might be the reason for the error message
mostafa.v68@xxxxxxxxx>got.
Best,
Zheyong
On Wed, Oct 16, 2019 at 4:42 PM Mostafa Valadkhani <
withwrote:
Hi
Sorry if I ask a lot and time to time. Actually I'm calculating SHC
results fromlammps using Kimmo Codes and wanna relate it somehow with the
followingGPUMD.
I wanna calculate SHC on the bilayer/monolayer graphene as your paper
with Ali.The attachments are my inputs, when I run the script
error comes up:
CUDA Error:
File: neighbor_ON1.cu
Line: 245
Error code: 700
Error text: an illegal memory access was encountered
can you give me some hints as always?
And I'm looking forward for your implementation of GKMA on GPUMD too.
Thanks,
M.V.
