Re: Volume Entry

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 16 2014 - 10:38:13 CST

On Sun, Feb 16, 2014 at 11:29 AM, Rawan Al Nsour <alnsourra_at_vcu.edu> wrote:
> Dr. Axel,
> I got the C4F10 experimental density, then I built the box volume based on
> that value. unfortunately, I got the message " the cell is too small"

there is far too little information in this one sentence to give any
kind of meaningful advice.

>
> On Mon, Feb 10, 2014 at 12:09 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Feb 10, 2014 at 12:04 PM, Rawan Al Nsour <alnsourra_at_vcu.edu>
>> wrote:
>> > First, many thanks for you sir for taking the time to reply.
>> > what I want to do is to find the density for small fluorocarbons such as
>> > c6f14, but it is very small molecule
>>
>> so what?
>>
>> please read my answer again, think about it for a bit and hopefully
>> you'll figure out where you are going in the wrong direction.
>>
>> axel.
>>
>> > On Mon, Feb 10, 2014 at 11:45 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> > wrote:
>> >>
>> >> please always copy the mailing list on your responses, so the
>> >> discussion gets properly archived and people can later look up the
>> >> outcome (and save time by not having to ask the same question).
>> >>
>> >> On Mon, Feb 10, 2014 at 11:25 AM, Rawan Al Nsour <alnsourra_at_vcu.edu>
>> >> wrote:
>> >> > Do you mean they are Zero
>> >>
>> >> or at best ill-defined.
>> >>
>> >> > then how can I find c6f14 density
>> >>
>> >> now *that* is a different question. density is computed from the total
>> >> mass in a reference volume. while it may be difficult to define the
>> >> reference volume for a single molecule, it is rather straightforward
>> >> to do so for a bulk system, provided you have a homogeneous
>> >> distribution of the density (at least at the scale and level of
>> >> accuracy that you are looking at). if you do not have a bulk system,
>> >> like in the case you are describing, you have to determine a suitable
>> >> reference volume yourself (e.g. through 3d-binning) and can try to
>> >> compute the density for this/these references through averaging.
>> >>
>> >> in short, you have to properly define what you are computing, because
>> >> what you are asking for is not well defined.
>> >>
>> >> axel.
>> >>
>> >>
>> >>
>> >> > On Mon, Feb 10, 2014 at 11:12 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> On Mon, Feb 10, 2014 at 11:08 AM, Rawan Al Nsour <alnsourra_at_vcu.edu>
>> >> >> wrote:
>> >> >> > I simulated a small molecule c6f14 without (PBC's and PME), I did
>> >> >> > not
>> >> >> > see
>> >> >> > the volume entry in the output file, how can I measure the volume?
>> >> >>
>> >> >> counter question: what is the volume of a point particle?
>> >> >>
>> >> >> bonus question: what is the volume of a collection of point
>> >> >> particles?
>> >> >>
>> >> >> axel.
>> >> >>
>> >> >> > Thanks
>> >> >> >
>> >> >> > --
>> >> >> > Rawan Al Nsour
>> >> >> > Ph.D. Candidate
>> >> >> > Department of Mechanical and Nuclear Engineering
>> >> >> > School of Engineering, Virginia Commonwealth University
>> >> >> > E-mail: alnsourra_at_vcu.edu
>> >> >> > 401 W. Main Street, Room E3216
>> >> >> > P.O. Box 843015
>> >> >> > Richmond, Virginia 23284-3015
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> >> >> College of Science & Technology, Temple University, Philadelphia PA,
>> >> >> USA
>> >> >> International Centre for Theoretical Physics, Trieste. Italy.
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Rawan Al Nsour
>> >> > Ph.D. Candidate
>> >> > Department of Mechanical and Nuclear Engineering
>> >> > School of Engineering, Virginia Commonwealth University
>> >> > E-mail: alnsourra_at_vcu.edu
>> >> > 401 W. Main Street, Room E3216
>> >> > P.O. Box 843015
>> >> > Richmond, Virginia 23284-3015
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> >> College of Science & Technology, Temple University, Philadelphia PA,
>> >> USA
>> >> International Centre for Theoretical Physics, Trieste. Italy.
>> >
>> >
>> >
>> >
>> > --
>> > Rawan Al Nsour
>> > Ph.D. Candidate
>> > Department of Mechanical and Nuclear Engineering
>> > School of Engineering, Virginia Commonwealth University
>> > E-mail: alnsourra_at_vcu.edu
>> > 401 W. Main Street, Room E3216
>> > P.O. Box 843015
>> > Richmond, Virginia 23284-3015
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
> Rawan Al Nsour
> Ph.D. Candidate
> Department of Mechanical and Nuclear Engineering
> School of Engineering, Virginia Commonwealth University
> E-mail: alnsourra_at_vcu.edu
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
>
>
>
>
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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