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Re: [lammps-users] nonpriodic boundry condition
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Re: [lammps-users] nonpriodic boundry condition


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 2 Oct 2017 07:00:31 -0400



On Mon, Oct 2, 2017 at 6:53 AM, Hossein Geraili <geraili.hsn@...36.....24...> wrote:


On Oct 2, 2017 1:58 PM, "Axel Kohlmeyer" <akohlmey@...24...> wrote:

>

>
>
> On Sun, Oct 1, 2017 at 10:24 PM, Hossein Geraili <geraili.hsn@...24...> wrote:

>>

>> Yes, you are right. It was an obvious misconception, but I have a last question. You said in the forum that total energy means nothing, and I need to calculate in this situation and use the total energy for another parameter calculation. So if I cannot calculate total energy for an ion pair at zero pressure in this was, what else can I do to calculate it?
>
> ​you are misquoting me. it is the _absolute value_ of the total energy, that has no meaning. that is not the same. total energy _differences_ are very much meaningful for as long as they are computed for the same setup, i.e. there are no changes that affect the total energy arbitrarily.
>
> axel.​
>
>

Thanks. So, there is no way to calculate comparable absolute total energy from lammps?

​of course there is. you are not understanding. 

axel.​

I need the absolute energy of one ion pair in nonperiodic boundary condition in specific temperatures to use it as an input( ideal contribution part of
Total energy in an energy formula derived from an equation of state)  for another parameter. Is there anyway to do that?
Best
>
>  


>>
>> Considering this information from the article that I work with:
>> "To calculate the cohesive energy
>>
>> density, the average internal energy and molar volume of the
>>
>> liquid were obtained from the liquid simulation, and the average
>>
>> internal energy of the ideal gas was obtained by simulating a
>>
>> single [bmim][PF6] ion pair at the same temperature as the liquid
>>
>> but at zero pressure (i.e., no periodic boundary conditions)."
>>
>> Best regards
>>
>>
>> On Oct 1, 2017 9:14 PM, "Hossein Geraili" <geraili.hsn@...24...> wrote:

>>>

>>> Dear Dr. Axel,
>>> I have this much information from article and there is no more than this almost anywhere. 
>>>
>>> "To calculate the cohesive energy
>>> density, the average internal energy and molar volume of the
>>> liquid were obtained from the liquid simulation, and the average
>>> internal energy of the ideal gas was obtained by simulating a
>>> single [bmim][PF6] ion pair at the same temperature as the liquid
>>> but at zero pressure (i.e., no periodic boundary conditions)."
>>>
>>> could you please help me with this exhausting issue. As you said it makes no sense to control temperature, but I need internal energy(total energy) in this temperature to calculate something else.
>>>
>>> Best regards
>>>
>>>
>>>
>>> Sent with Mailtrack
>>>
>>> Virus-free. www.avast.com
>>>
>>> On Sun, Oct 1, 2017 at 8:46 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

>>>>

>>>>
>>>>
>>>> On Sun, Oct 1, 2017 at 12:03 PM, Hossein Geraili <geraili.hsn@...24...> wrote:

>>>>>

>>>>> Dear lammps users,
>>>>> How can I control the temperature in nonperiodic boundary condition without controlling volume with NVE?
>>>>
>>>>
>>>> ​please note, that there is a significant difference between using fix nve and an NVE ensemble. you *can* achieve an NVE ensemble by using fix nve, but using fix nve does not automatically result in an NVE ensemble. this has been explained on this mailing list many, many times.
>>>>
>>>> besides, fix nve does *NOT* control the volume. ​ in fact, to be compatible with creating an NVE ensemble is *MUST NOT* do *any* manipulations of the system, neither volume nor (kinetic) energy.
>>>>
>>>> ​​fix nve is fully compatible with non-periodic boundaries. 
>>>>  


>>>>>
>>>>> I want to calculate density at the ideal gas state, so I need to control temperature, but thermostats have no time integration.
>>>>
>>>>
>>>>
>>>> however, you are not making much sense here. using a thermostat for an ideal gas is pointless, since ideal gas particles do not interact; so how could they couple with a reservoir?
>>>>
>>>> ​also, there is not such thing as an "ideal gas state". an ideal gas is a well defined thermodynamic entity. there is little value to doing simulations of an ideal gas, since all its properties can be obtained analytically.
>>>>
>>>> besides, what has this all to do with periodic-boundary conditions?
>>>>
>>>> axel.
>>>>
>>>>
>>>>
>>>>  


>>>>>
>>>>> best regards 
>>>>>
>>>>> --
>>>>> Hosein Geraili Daronkola
>>>>> M.Sc.Graduated of physical chemistry
>>>>> Physical Chemistry,
>>>>> Department of Chemistry,
>>>>> Sharif University of Technology.
>>>>> geraili_hosein@...7110...
>>>>>
>>>>>
>>>>>
>>>>> Sent with Mailtrack
>>>>>
>>>>> Virus-free. www.avast.com
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>> _______________________________________________
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>>>>> lammps-users@...396...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.
>>>
>>>
>>>
>>>
>>> --
>>> Hosein Geraili Daronkola
>>> M.Sc.Graduated of physical chemistry
>>> Physical Chemistry,
>>> Department of Chemistry,
>>> Sharif University of Technology.
>>> geraili_hosein@...7110...
>>
>>
>
>
>
> --
> 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@...92......  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.