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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: Wed, 19 Jul 2017 00:32:19 -0400

On Tue, Jul 18, 2017 at 11:44 PM, vo thuy phuong Vo
<thuyphuongqnu@...24...> wrote:
> Dear Axel,
> So sorry that some mistake in the input file, I mean addforce in the inner
> region -20, outer 10 and 10. Anyway, I try my input file with and without
> fix addforce command and the results are exactly the same. I think maybe my
> system is unphysical or some thing else? I am so confused.

i think you may be underestimating the strength of interactions in a
dense system.

> Could you please
> suggest me any simple example that can work well with fix_addforce command
> for region?

there are examples in the obstacle and flow folders that used fix
addforce. it is easy to modify them to use regions.
if you want to be productive as a researcher, you have to devise your
own examples. i suggest you start with a diluted system with purely
repulsive interactions and then try simple manipulations unless you
have a sense for what you can do and how the system reacts. then you
can gradually change it to more closely resemble your system of
interest.

axel.




> Thank you very much and wish you a good day.
>
> Best,
>
> Phuong.
>
> 2017-07-18 15:57 GMT+10:00 vo thuy phuong Vo <thuyphuongqnu@...24...>:
>>
>> Dear Axel,
>> So sorry that confusing you. Yes, I want to compress the atoms in the
>> inner region. I will describe them again. I would like to see the
>> condensation (or higher density of particles) in the inner regions so I use
>> fix addforce for atoms only in the inner region. I have add forces to the
>> outer regions also with opposite sign. However, the obtained output shows me
>> that the number of atoms in the inner region is not higher than outer1
>> region. Could you suggest me which wrong with my assumption and is there any
>> possible way or command in Lammps that I could do it?
>> Thank you very much.
>>
>> Here is my input
>> units                         real
>> atom_style            atomic
>> boundary               p p p
>> 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 70 105
>> 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       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 20 region inner
>> fix           3 all addforce 0 0 -10 region outer1
>> fix           4 all addforce 0 0 20 region outer2
>> 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
>>
>> Have a good day.
>>
>> Phuong
>>
>> 2017-07-17 22:20 GMT+10:00 Axel Kohlmeyer <akohlmey@...24...>:
>>>
>>> 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
>>>
>>> i cannot follow your reasoning here. you are adding a constant force
>>> in z-direction to the atoms in the inner region.
>>> that will accelerate all of them in z-direction. nothing more. the
>>> result should be to induce a flow in z-direction.
>>> if you want to compress the atoms in the inner region, you have to add
>>> forces to the atoms in the two *outer* regions with opposite sign.
>>>
>>> axel.
>>>
>>> > 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 <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.
>>
>>
>



-- 
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.