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Re: [lammps-users] Question about set up step potential in gcmc lammps

Re: [lammps-users] Question about set up step potential in gcmc lammps

 From: vo thuy phuong Vo Date: Mon, 17 Jul 2017 17:36:59 +1000

Dear Lammps-users,
I just noticed that my input has problem with the variable num (it should be v_num). However, the results seems do not look like what I expect. I would like to create an extra force only in the inner region, then if the atoms move out of other regions, this force will be disappeared. Therefore, if everything is fine, the number of atoms in the inner region has be to larger than others. That's why I am so confused
1. How can I set up the extra force only for the inner region?
2. Why the total number of all region (r1) is not equal when I sum them all from different regions (outer and inner)?
units                         real
atom_style            atomic
boundary               p p p
lattice                       sc 0.5
region                r1 cylinder z 0 0 5 0 100
region                outer1 cylinder z 0 0 5 0 35
region                inner  cylinder z 0 0 5 35 70
region                outer2  cylinder z 0 0 5 70 100
create_box            1 r1
mass                         1 16.0425
pair_style               lj/cut 10.0
pair_coeff              1 1 0.2943 3.81 10.0
#group  ch4  type 2
thermo                    1000
compute_modify thermo_temp dynamic yes
variable       chempot equal -2000
#variable       density equal atoms/vol
variable       num equal count(all,outer1)
variable       num2 equal count(all,outer2)
variable       num3 equal count(all,inner)
variable       chempotkcal equal \${chempot}/503.219
fix            1 all addforce 0 0 -100.0 region inner
fix            2 all gcmc 1 100 100 1 29494 300.0 \${chempotkcal} 0.5
thermo_style   custom step atoms temp pe ke etotal press vol v_chempot density atoms v_num v_num2 v_num3
run            100000

Thank you very much and so sorry for my question. It may be obvious but I just start with Lammps and still feel confused. I have tried but cannot solve them by myself.

Best,

Phuong.

2017-07-17 16:14 GMT+10:00 vo thuy phuong Vo :
Dear Axel,
Thank you very much for your help. I have made an input and set up an extra force. I would like to see the different number of particles in different regions so I use the command count(ID, region). However, the error was shown that no atoms in group ch4. Could you please help me to figure out this? I try to take a look in the manual as well as other questions but everything seems normal.
Here is my input (I just set up all the values randomly because I just want to check how it works)
units                         real
atom_style            atomic
boundary               p p p
lattice                       sc 0.5
region                r1 cylinder z 0 0 5 0 100
region                outer1 cylinder z 0 0 5 0 35
region                inner  cylinder z 0 0 5 35 70
region                outer2  cylinder z 0 0 5 70 100
create_box            1 r1
mass                         1 16.0425
pair_style               lj/cut 10.0
pair_coeff              1 1 0.2943 3.81 10.0
group  ch4  type 1
thermo                    1000
compute_modify thermo_temp dynamic yes
variable       chempot equal -2000
variable       density equal atoms/vol
variable       num1 equal count(ch4,outer1)
variable       num2 equal count(ch4,outer2)
variable       num3 equal count(ch4,inner)
variable       chempotkcal equal \${chempot}/503.219
fix            1 all addforce 0 0 -2.0 region inner
fix            2 all gcmc 1 100 100 1 29494 300.0 \${chempotkcal} 0.5
thermo_style   custom step atoms temp pe ke etotal press vol v_chempot density atoms num1 num2 num3
run            10000
Thank you very much.

Phuong.

2017-07-13 13:45 GMT+10:00 Axel Kohlmeyer :
On Wed, Jul 12, 2017 at 11:39 PM, vo thuy phuong Vo
<thuyphuongqnu@...24...> wrote:
> Hello Axel,
> Thank you for your help. As I read in the manual, I can set up region with
> different parameters (pressure, chemical potential). However, in this case,
> I want to keep these parameters same in two regions. In stead of set up
> different pressure or chemical potential, could I set up an external
> potential within a certain region that can help my lennard-jones particles
> confined in that region? Could I use the fix addforce command to do this? I
> plan to add an external force for particles if they move into particular
> region and without external force for other region. Is it possible?

this is different from what you asked before.
sure you can define an additional confinement potential.
fix addforce is one option, fix wall/region is another.

axel.

> Thank you very much!
>
> Best,
>
> Phuong
>
> 2017-07-10 21:08 GMT+10:00 Axel Kohlmeyer <akohlmey@...24...>:
>>
>> On Sun, Jul 9, 2017 at 11:47 PM, vo thuy phuong Vo
>> <thuyphuongqnu@...24...> wrote:
>> > Dear Lammps-users
>> > I am a new user Lammps and would like to perform gcmc using fix gcmc
>> > command
>> > in lammps. My system is a cylinder in which the middle region is put a
>> > deeper potential then outer region. As the definition of chemical
>> > potential
>> > in gcmc:
>> > mu=ln(particle density) + beta*potential.
>> > I would like to control mu constant by gcmc but the middle region has
>> > deeper
>> > potential so that the particles will be more in this region. I wonder
>> > can
>> > lammps support this feature which we can set up the different potential
>> > for
>> > different region (so that the obtained density particles will be
>> > different
>> > too) in gcmc (chemical potential is controlled to be constant)?
>> > As I look in the manual, we can set up different pressure but in this
>> > case,
>> > I would like to use the step potential for my system. Is it possible?
>> > Thank
>>
>> you can define two target regions (the inside and the outside of your
>> cylinder) and then set up two fix gcmc commands with different
>> parameters, each restricted to one of the two regions.
>>
>> axel.
>>
>> > you very much.
>> >
>> > Best,
>> >
>> > Phuong
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
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>> >
>>
>>
>>
>> --
>> 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.

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