LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] fix NPT and fix move
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] fix NPT and fix move


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 12 Apr 2018 04:38:47 -0400

On Thu, Apr 12, 2018 at 2:06 AM, liyi bai <liyibai2011@...24...> wrote:
> Dear Axel,
>
>
> On the one hand, I don't want the two plates move.Then I use fix move
> command.
> As I use NPT,the box length will be changed along x y z direction.The point
> is I ONLY the box length change on z direction NOT x or y.So that I want to
> control pressure on z direction.
>
> I replace"dilate all" as "dilate water".The water will still go through the
> plate and finally move to other pbc box.I am confused what happened here.

there is not much of a confusion, in my opinion. LAMMPS is behaving
the way it is programmed.
the problem is, like i already mentioned, that you are asking for
something that is contradicting itself, is physically impossible, and
thus makes no sense.

axel.

>
> Thank you very much for your attention.
>
> partial input :
>
> group       plate1       type 4
> group       water        type 1 2
> group       plate2       type 3
>
> variable    fx equal  fcm(plate2,x)
> variable    fy equal  fcm(plate2 ,y)
> variable    fz equal  fcm(plate2 ,z)
>
>
> #---------------------------------------------------------------
> # stage 4 :NPT ensemble
> #---------------------------------------------------------------
>
> fix      6   water   shake 0.0001 20 0 b 1 a 1
> fix      7   water   npt temp $T $T 100.0  z 1.0 1.0 100.0 dilate water
>
> fix      8   plate1  move linear 0.0 0.0 0.0 units box
> fix      9   plate2   move linear 0.0 0.0 0.0 units box
>
> thermo_style     custom  v_time v_fx v_fy v_fz press vol temp evdwl ecoul
> etail elong pe ke lx ly lz xlo xhi ylo yhi zlo zhi xy xz yz
> thermo            5
>
> 2018-04-12 12:49 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:
>>
>> On Wed, Apr 11, 2018 at 10:49 PM, liyi bai <liyibai2011@...24...> wrote:
>> > Dear Axel,
>> >
>> > Thank you very much for your suggestion and kindly remind.
>> >
>> > I also tried to leave "fix move" away.But the plates will be change the
>> > position which I should avoid the situation .
>>
>> then you should not use "dilate all" with fix npt.
>>
>> > Actually, I want to control the distance between two plates as a
>> > constant.So
>> > the position most not be moved.That's why I want to use fix move to fix
>> > the
>> > two plates.In detail,  lateral size of one larger plate as same as box
>> > size,other plate is much smaller  the boxsize.
>> >
>> > I want to  keep the lateral size of  the box always as a constant I set
>> > up
>> > initially.For that, I adjust the system pbc only on Z direction during
>> > npt
>> > simulation by using below command line.However,the water will go through
>> > the
>> > plate and goes to other pbc box during NPT.Could you please point out
>> > some
>> > problems about the issue?
>>
>> i don't understand what you are doing here. on one hand you say, you
>> don't what the plates to move, but on the other hand, you want to
>> control the pressure in the same direction. that contradicts each
>> other and thus makes no sense.
>>
>>
>> axel.
>>
>> >
>> > fix      7   water   npt temp $T $T 100.0 z 1.0 1.0 100.0  dilate all
>> >
>> >
>> >
>> > Thank you very much
>> >
>> >
>> > best wishes
>> >
>> > Liyi
>> >
>> >
>> >
>> >
>> >
>> > 2018-04-11 22:43 GMT+09:00 Axel Kohlmeyer <akohlmey@...24...>:
>> >>
>> >> On Wed, Apr 11, 2018 at 9:35 AM, liyi bai <liyibai2011@...24...>
>> >> wrote:
>> >> > Dear all.
>> >> >
>> >> > I want to run MD simulation with NP(z)T ensemble for system of two
>> >> > plates
>> >> > immersed in water.
>> >> >
>> >> > I am wondering that the correct way combine fix npt  and fix move
>> >> > command.
>> >>
>> >> there is no point in using fix move, when you don't move the atoms.
>> >> you can just leave those fixes away.
>> >>
>> >> >
>> >> > I wrote input below,I am not sure if it is correct. Can any one give
>> >> > me
>> >> > some
>> >> > suggestion?
>> >>
>> >> if you are not sure that something is working as expected, you should
>> >> construct test cases and monitor those carefully to see, if things
>> >> happen to your expectations. with carefully crafted tests, you can
>> >> check each feature you worry about individually.
>> >>
>> >> asking the mailing list to help you with this is very risky. what if
>> >> the person responding makes a mistake? or overlooks something
>> >> important? or you are leaving out important information that would
>> >> have resulted in a different recommendations?
>> >> it is always your reputation and credibility that is on the line, if
>> >> you use your results in publications, so you need to verify for
>> >> yourself that you are simulating what you think and want to do.
>> >>
>> >> axel.
>> >>
>> >> >
>> >> >
>> >> > fix      6   water   shake 0.0001 20 0 b 1 a 1
>> >> > fix      7   water   npt temp $T $T 100.0 z 1.0 1.0 100.0  dilate all
>> >> > #
>> >> > control system only on z direcation
>> >> >
>> >> > fix      8   plates1       move linear 0.0 0.0 0.0 units box   #fix
>> >> > plates 1
>> >> > fix      9   plates2       move linear 0.0 0.0 0.0 units box   #fix
>> >> > plates 2
>> >> >
>> >> >
>> >> > Thank you very much
>> >> >
>> >> > best wishes
>> >> >
>> >> >  liyi
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > 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.