[gmx-users] Getting the virial for each individual atom.

[Timothy Sirk]

Zach,

If you aren't using PBC, then how about saving total forces per atom and
use 'ri outer Fi' for the per-atom virial? And, if you want it, get the
kinetic part from 'm* (vi outer vi)'.

The virial shouldn't have to come from ij pairs, although that is certainly
a good way to get it.

Tim

On Tue, Jan 22, 2013 at 11:05 AM, Marcin, Zachary <zachary.marcin at wilkes.edu
> wrote:

> Tim,
> The PBC's were turned off and need to be for what we're trying to do.
> Pretty much everything that might work, as far as I've seen, can't unless
> we change some source code to do what we need.
> Thanks,
> Zach
>
> On Mon, Jan 21, 2013 at 4:47 PM, Timothy Sirk <tsirk at vt.edu> wrote:
>
> > Zach,
> >
> > Do you have periodic system with charges? For PBC, you might try one of
> the
> > forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more
> work...
> > For Ewald sum and PPPM contribution, you could check refs in
> > lammps.sandia.gov/doc/PDF/kspace.pdf
> >
> > We have an upcoming paper that explains in more detail how to do this
> with
> > PPPM and gives an example with heat flux. Maybe something similar could
> be
> > done in GROMACS with PME.
> >
> > best,
> >
> > Tim
> >
> >
> > On Mon, Jan 21, 2013 at 1:06 PM, Marcin, Zachary
> > <zachary.marcin at wilkes.edu>wrote:
> >
> > > Berk,
> > > Here is where I think I might be able to:
> > > In calcvir.c there is a method called calc_vir which takes, among other
> > > things, int nxf(no idea what this does), rvec x[], and revec f[].  It
> > then
> > > does dvxx+= x[i][xx] *f[i][XX];.
> > > This is the same as the formula that I am trying to solve for (Vi*Pi +
> > > .5*SUM(Rij * Fij)).
> > > What I figured I could do is create another array to calculate the
> > virials
> > > for, thus giving me an index position per atom, and then use that
> > somehow.
> > >
> > > I also know that I can use R(ij) * F(ij), or the distance between
> atoms i
> > > and j times the Forces between atoms i and j.  If anyone has any
> insight
> > on
> > > getting these, that could also work.
> > > I know how to get the individual positions, but I don't know how I
> would
> > go
> > > about the forces aspect of that.
> > >
> > > Thanks,
> > > Zach
> > >
> > > On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> > >
> > > >
> > > > Hi,
> > > >
> > > > The virial has no meaning per atom.
> > > > And you can't get the virial per atom out of Gromacs, it is never
> > > > calculated in that way (see the manual for details).
> > > > A special local pressure version of Gromacs exists, but even there
> you
> > > > won't get a virial per atom.
> > > >
> > > > Cheers,
> > > >
> > > > Berk
> > > >
> > > > ----------------------------------------
> > > > > Date: Mon, 21 Jan 2013 12:35:04 -0500
> > > > > From: zachary.marcin at wilkes.edu
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: [gmx-users] Getting the virial for each individual atom.
> > > > >
> > > > > Hello,
> > > > > For the research I'm working with, I need to get the virial for
> each
> > > > > individual atom in the system. I've been tracing all of the calls
> > made
> > > in
> > > > > the methods related to virials(Version 4.5.5) and this is the call
> > > stack
> > > > > that I think has what I need.
> > > > > mdrun.c -> do_md in md.c -> do_force in sim_util.c -> calcvir.c
> > > > >
> > > > > I have a few questions that I was wondering if anyone could answer.
> > > > >
> > > > > 1. In sim_util.c, there is a comment that says "Total virial
> computed
> > > in
> > > > > global_stat, called from do_md". I cannot find where this is called
> > in
> > > > > do_md. Was this changed at any point and the comment was still left
> > in
> > > > the
> > > > > code?
> > > > >
> > > > > 2. If I change the codes in calcvir.c to find the virials for each
> > > > > individual atom, say by piping the atom numbers and forces and
> > > everything
> > > > > needed into another program so it doesn't effect the way that
> gromacs
> > > > runs
> > > > > and will still allow everything to do what it needs, will this be
> > > screwed
> > > > > up by/screw up the domain decomposition/the mpi stuff?
> > > > >
> > > > > Basically, I'm looking for advice on a method to output the
> > individual
> > > > > virials for each atom for each frame, instead of just the final
> > output
> > > of
> > > > > the average virial on the entire system.
> > > > > Thanks,
> > > > > Zach Marcin
> > > > > Wilkes University
> > > > > --
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