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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 17 Jul 2017 08:17:07 -0400

On Mon, Jul 17, 2017 at 3:36 AM, vo thuy phuong Vo
<thuyphuongqnu@...24...> wrote:
> 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?

you did.

> 2. Why the total number of all region (r1) is not equal when I sum them all
> from different regions (outer and inner)?

because your simulation box is *not* the volume of region r1 but the
orthogonal volume enclosing it.


axel.

> 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 <thuyphuongqnu@...24...>:
>>
>> 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 <akohlmey@...24...>:
>>>
>>> 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
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > ------------------------------------------------------------------------------
>>> >> > Check out the vibrant tech community on one of the world's most
>>> >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> >> > _______________________________________________
>>> >> > lammps-users mailing list
>>> >> > lammps-users@lists.sourceforge.net
>>> >> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> 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.
>>
>>
>



-- 
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.