Dear All users,
I want to calculate the number density for my molecules. I need to calculate the number
density for center of masses of my molecules not atoms of my molecules. Is it possible by
LAMMPS? If not, are there any post processing utilities for calculating this parameter?
Thanks in advance.
Dear All users,
I want to calculate the number density for my molecules. I need to calculate
the numberdensity for center of masses of my molecules not atoms of my molecules. Is
it possible byLAMMPS? If not, are there any post processing utilities for calculating this
parameter?
my preferred post processing utility for this task is called "pocket
calculator".
axel.
Try this:
variable numberdensityofmolecules equal 42/vol # units are molecules/distance^3
If you do not have 42 molecules, this won't be especially accurate.
Dear Aidan and Axel,
Thank you very much for your reply. I left an unclear post.
I mean I want to record a number density profile which is related to COMs instead of atoms.
I want to record the positions of my molecules in each snapshot and then calculate the average over all of my snapshots just similar
to ave/spatial command which can calculate the density/mass or number/density. This command records atoms not COMs of molecules.
How can I do this? I need sum clues for starting writing cpp code.
Thanks in advance.
The compute com/molecule command will calculate the COM of each
molecule. It cannot be used as input to fix ave/spatial, but you
can output it to a file via fix ave/time with the vector option. Then
post-process it to do your own spatial averaging.
Steve
The compute com/molecule command will calculate the COM of each
molecule. It cannot be used as input to fix ave/spatial, but you
can output it to a file via fix ave/time with the vector option. Then
post-process it to do your own spatial averaging.
probably not worth the effort. since using the COM. is already quite
an approximation over using all (heavy) atom positions, it usually
doesn't make a difference beyond the statistical (and systematic)
error to simply pick the one atom in the molecule that is closest to
the COM. define a suitable group, and use fix ave/spatial directly.
axel.
Dear Steve and Axel,
Thank you very much for your replies.
To Steve: I performed an NVT ensemble including the Steve Suggestion yesterday but I
have not analyze my outputs from ave/time. I got an warning which revealed that my group has atoms not in the group while my group
included all of the atoms(1888 atoms with out any atoms beyond my group)
To Axel: I want to know your method is acceptable in a scientific article? before my supervisor suggested me doing this method but which atoms?
For example in Heptane molecules which one should I chose? middle carbon? besides, I will have problems with rdf calculation. After all, I want to
calculate the rdf for COM-COM of my molecules instead of atom-atoms of my molecules.
To Axel: I want to know your method is acceptable in a scientific article?
how *can* you know? make a *&%#&$ test!
before my supervisor suggested me doing this method but which atoms?
see above
For example in Heptane molecules which one should I chose? middle carbon?
besides, I will have problems with rdf calculation. After all, I want to
see above
calculate the rdf for COM-COM of my molecules instead of atom-atoms of my
molecules.
see above.
as i said, using the COM is as artificial a measure as picking a
(random or specific) atom. i am not saying that you *have* to do it,
but that you *may* be able to do it. how good a choice one over the
other is depends very much on the choice of system and molecule.
research doesn't work by blindly doing what you get told. if that were
the case, it would be much easier and cheaper to have a bunch of
robots do the work your are trying to do. you have to use that stuff
sitting between your ears every once in a while, too.
axel.
Dear Axel,
I really can not understand your intention. Anyway, I suggest you teaching philosophy of science.
I will attend your class surely.
Dear Axel,
I really can not understand your intention.
my intention is to teach you something that is called "problem
solving", and to that end make you try other problem solving
strategies than just asking questions until people give up on you.
axel.
Anyway, I suggest you teaching philosophy of science.
I will attend your class surely.
and make certain that i commit suicide??
What Axel is trying to say is : “One cannot take a chicken into the water”.
Above, the “chicken” being you and the “water” the atomistic simulations field.
Learn quickly in life what your strengths and limitations are and avoid drowning in the water.
Carlos
Dear Axel and Carlos,
To Axel: Okay, I will not attend. Our mailing list needs you.
I think I can understand your intentions I love this field of study and will continue it for finding out more and more.
I am warming up at the beginning point.
Sometimes I wonder if you are the artificial brain Ray Kurzweil is building at google. Lots of perseverance but little common sense. Anyways, do as you please. Its your life. I would be very glad for you if you were to prove me wrong.
Carlos