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Re: [lammps-users] region command with block &union argument
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Re: [lammps-users] region command with block &union argument


From: Julien Guénolé <julien.guenole@...4839...>
Date: Sat, 2 Dec 2017 17:38:10 +0100

Le 01/12/2017 à 11:40, liyi bai a écrit :
Dear Users,

Thank you very much for your reply. Sorry,I just realized  I have only send individual person.

I don'y use create_atom command.Which part in log file,should I check?

So how do you get atoms in your simulation box? By using read_data?
Ensure that your _entire_ simulation box is filled with atoms, and not only the region sideplate. Otherwise, changing sideplate  will not change the quantity of selected atoms...

Julien

Thank you very much for your help.


Best Wishes

Liyi

2017-12-01 19:15 GMT+09:00 Julien Guénolé <julien.guenole@...4839...>:
On 01/12/17 03:31, liyi bai wrote:
Dear Users.

Thank you very much for your promptly reply.


My simulation box size as below:

     0.000000000    62.000000000 xlo xhi
     0.000000000    62.000000000 ylo yhi
     0.000000000    53.000000000 zlo zhi 

partial input:

region      sideplate  block  13.94 47.94 13.94 47.94 16.0 30.783 side in
region      
sidetip    sphere 30.94 30.94 30.783  9 side out
region      
myconfined  union sideplate sidetip

group       
myregion   region  myconfined


dump         2  myregion  custom 5  layer2ns10dt.$a id type x y z vx vy vz

dump_modify   2   region myconfined sort id  


I wanna specify the region(blue region in figure 1,origin color is my simulation box) between two solid(the hemisphere over the center of plate with some distance,the space between hemisphere and plate was the region I wanna define).The plate with lateral size x*y*z=34*34*1.783 (as I shown above 34=xhi-xlo=47.94-13.94), the height space over plate I defined is (14.783=zhi-zlo=30.783-16.0).The center of hemisphere is x,y,z=30.94 30.94 30.783.

If I change R=9 to R=16,the total number of dumped atoms will be change.However,the total number of dumped atoms will not change by changing the x,y of plate, like xlo=13.94 to xlo=0 ,xhi=47.94 to xhi=40.

To help you on this particular point, the log file itself will give precious information. Never assume the script will work as intended: always check with the log that IT IS actually working as intended. For example, what about the create_atom command?

Also, always reply to the list. Thanks!

Julien.



I would like to know how to define the region above plate as show blue color in figure 2.I did not find any strange information in log file.

partial dump file  for R=9:

ITEM: TIMESTEP

5

ITEM: NUMBER OF ATOMS

20521

ITEM: BOX BOUNDS pp pp pp


partial dump file  for R=20:


ITEM: TIMESTEP

5

ITEM: NUMBER OF ATOMS

17961

ITEM: BOX BOUNDS pp pp pp


figure 1



​ figure 2



2017-12-01 3:30 GMT+09:00 Julien Guénolé <julien.guenole@...4839...>:
I do not see a particular problem in the command you copied here.
Could you post the part of your parameter and log that describes the construction of the system, regions and groups?


On 30/11/17 14:51, liyi bai wrote:
Dear Users,
 

I wanna dump the atoms in specified region.The total number of dumped atoms can be change with radius R.However,the total number of dumped atoms can not be changed with the lateral size of plate.
Like, If I change R=10 to R=20.The dumped atoms will be decreased. If I change the plate lateral size X=40 to X=60 and  Y=40 to Y=60,the total number of dumped atoms can not be change.

Is there any one knows what's wrong with my specified region shown below.Any suggestions are 
appreciated.

partial input :

region      sideplate  block  40 0 40 0 30 side in
region      
sidetip    sphere 20 20  30 10(R) side out
region      
myregion  union 2 sideplate sidetip


Thank you very much


Best Regards


Liyi Bai