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.mar...@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 <ts...@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.mar...@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 <g...@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.mar...@wilkes.edu > > > > > To: gmx-users@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 > > > > > -- > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > > * Please don't post (un)subscribe requests to the list. 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Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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