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Re: [lammps-users] damp fix press/berendsen and fix langevin
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Re: [lammps-users] damp fix press/berendsen and fix langevin


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 7 Jul 2017 14:53:06 -0400

On Fri, Jul 7, 2017 at 12:41 PM, ruiyan <r-yan14@...61...> wrote:
> Dear Axel,
>
> Thanks a lot for your reply. Every explanation from you helps me to
> understand commands themselves or to know the direction I should go. Thank
> you very much.
>
> As for modulus keyword in fix press/berendsen, from lammps manual, the bulk
> modulus has units of pressure and is the amount of pressure that would need
> to be applied (isotropically) to reduce the volume of the system by a factor
> of 2 (assuming the bulk modulus was a constant, independent of density,
> which it's not). This means we can't get an accurate modulus value  easily
> since it's not a good choice to half the volume of the system and see what
> the pressure is. Combined with fix nve and fix langevin, I tried two groups
> of Pdamp and modulus in fix press/berendsen. In the first group,
> Pdamp*modulus=100, while in the seconde group Pdamp*modulus=1000. I found
> that in both groups, pressures reach their average values quickly. The
> difference is that average value in the first condition is far from the
> target pressure specified in fix press/berendsen and pressure fluctuates
> widely, while in the seconde condition, average pressure is very close to
> the target value and fluctuation is very small. Pdamp should only affect the
> time when pressure reaches to the target value and the extent of pressure
> fluctuation , why is the pressure in the first condition far from the target
> value and doesn't show any trend to close to the target one?

your expectations would only apply to an ideal gas. for real systems,
and particularly dense system, things are much more complicated and if
you choose a bad combination of parameters, you can, for example, get
a "feedback loop".

specifically, if the time constant is small, the volume adjustments
can be too large, and since it is always easier to quickly expand a
dense system than to rapidly compress a dilute system back to its
dense state at a given average pressure, the average can be easily
off.

axel.


>
> Thanks for your suggestion. I need to read some materials on langevin
> dynamics in general to have a better understanding in this command.
>
> Thanks again and look forward to your reply.
>
> Best wishes,
>
> Rui
>
>> -----原始邮件-----
>> 发件人: "Axel Kohlmeyer" <akohlmey@...24...>
>> 发送时间: 2017-07-07 22:56:38 (星期五)
>> 收件人: ruiyan <r-yan14@...61...>
>> 抄送: "LAMMPS Users Mailing List" <lammps-users@...431...ceforge.net>
>> 主题: Re: [lammps-users] damp fix press/berendsen and fix langevin
>
>>
>> On Fri, Jul 7, 2017 at 7:06 AM, ruiyan <r-yan14@...61...>
>> wrote:
>> > Dear all,
>> >
>> > I have several questions related to fix press/berendsen command and fix
>> > langevin command.
>> >
>> > 1. In fix press/berendsen command, we need to specify Pdamp and modulus
>> > value. From lammps manual of 2016Nov17, the recommneded value for Pdamp
>> > is
>> > 1000 timesteps, but I don't know what modulus mean in this command? Do
>> > we
>> > need to specify modulus value according to the real modulus of the
>> > material
>> > we simulate? Or we just need to consider the product of Pdamp and
>> > modulus to
>> > make pressure relax in a reasonable rate?  If the latter one is
>> > correct, is
>> > there a recommend value for modulus?
>>
>> please have a more careful look at the documentation for fix
>> press/berendsen. all your questions are answered.
>>
>>
>> > 2. In fix langevin command,
>> >
>> > (1) how to specify Tdamp? I don't find a recommended value for it.
>>
>> that is impossible to provide, because it depends on how you are using
>> fix langevin. you need a different Tdamp when you use fix langevin an
>> explicit solvent system or implicit solvent (and different solvents to
>> boot).
>>
>> > (2) Especially how to specify scale values? I know that the mass and
>> > size of
>> > different atom types should be accounted for in the choice of ratio
>> > values,
>> > but how? Suppose I define two atom types in my simulation box.
>> > Condtion1,
>> > for type1, mass=1, size=1, and type2, mass=1, size=2, what are sacle
>> > values
>> > for type1 and type2?
>>
>> again, this strongly depends on the kind of simulation you are doing,
>> you may not need to set it at all.
>> at any rate, you need to read the documentation carefully, if you have
>> trouble understanding the details, you probably also need to read up
>> on langevin dynamics in general.
>>
>> please note, that the LAMMPS manual is a "technical documentation",
>> i.e. it will tell you what the commands and keywords stand for, but
>> its purpose is not to explain the physics or tell you exactly how to
>> do your research (and neither is it the purpose of the mailing list).
>> think of it being like the owner's manual of a car: it tells you where
>> all the switches, buttons and levers are, but you still have to go to
>> driving school to learn how to drive.
>>
>> axel.
>>
>> > (3) Condition2, for type1, mass=1, size=1, and type2, mass=2, size=1,
>> > what
>> > are sacle values for type1 and type2?
>> >
>> > (4) Condition3, for type1, mass=1, size=2, and type2, mass=4, size=1,
>> > what
>> > are sacle values for type1 and type2?
>> >
>> >
>> > Thanks and look forward to your reply.
>> >
>> > Rui
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
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>> > _______________________________________________
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>> > lammps-users@lists.sourceforge.net
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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.