[gmx-developers] adding external forces to all atoms

[Semen Esilevsky]

Dear Julius,
That's really cool! Thank you very much for sharing this solution! 

I thing mdlib/domdec.h and mdlib/domdec.c should be officially patched to allow such things.

Regards,
Semen




>________________________________
>From: Julius Su <jsu at caltech.edu>
>To: gmx-developers at gromacs.org
>Sent: Saturday, October 15, 2011 12:50 AM
>Subject: [gmx-developers] adding external forces to all atoms
>
>Hi everyone,
>
>I would like to present a solution I've arrived at to implement a feature -- the ability to add a set of external forces F(x1 ... xN) to all the atoms of a parallel GROMACS simulation -- which has been previously discussed:
>
>http://lists.gromacs.org/pipermail/gmx-developers/2011-May/005193.html
>http://lists.gromacs.org/pipermail/gmx-developers/2011-April/005141.html
>
>This could useful for applying biasing potentials that span decomposition domains, such as ones acting on collective coordinates, or for applying novel experimental restraints which include large groups of atoms in the system. There is existing functionality in GROMACS to do this sort of thing, but the code below makes it straightforward to try out different potentials, without needing to perform a more extensive integration with the existing code base. So it may be useful for prototyping purposes ..
>
>Note that in the approach below, all the work for evaluating F(x1 ... xN) is localized to one processor (the Master), so it should not a time consuming potential to evaluate -- else the parallel benefits of GROMACS are negated. Also the synchronization required to evaluate and distribute the forces may cause the parallel performance to suffer slightly.
>
>In any case, since there appears to be some (scattered) interest, I'll present my code modifications. They may be of use to others in the community. Also if I've done anything egregiously (or even slightly) wrong, please let me know!
>
>Sincerely,
>
>Julius
>
>-----
>(1) In kernel/md.c, modify such that f_global is always initialized:
>
>        //if (DDMASTER(cr->dd) && ir->nstfout) {
>        if (1) {                                 // change so that f_global is always initialized
>            snew(f_global,state_global->natoms);
>
>(2) In kernel/md.c, add lines in
>
>       /*  ################## END TRAJECTORY OUTPUT ################ */
>
>       // Collect all
>       if (DOMAINDECOMP(cr))
>          dd_collect_vec(cr->dd, state, f, f_global);
>
>        if (MASTER(cr))
>        {
>           // Fetch positions of all atoms
>          for (i = 0; i < state_global->natoms; i++)
>          {
>            current_x[i] = state_global->x[i][0];
>            current_y[i] = state_global->x[i][1];
>            current_z[i] = state_global->x[i][2];
>          }
>
>          // Compute biasing potential (ADD NEW POTENTIAL HERE)
>          ... Given current_x, current_y, current_z --> returns delta_fx, delta_fy, delta_fz.
>
>          // Apply biasing potential to all atoms
>          for (i = 0; i < state_global->natoms; i++)
>          {
>             f_global[i][0] += delta_fx[i];
>             f_global[i][1] += delta_fy[i];
>             f_global[i][2] += delta_fz[i];
>          }
>        }
>
>        // Distribute modified f_global back to individual processors
>        if (DOMAINDECOMP(cr))
>          dd_distribute_vec(cr->dd, dd_charge_groups_global(cr->dd), f_global, f);
>
>        // Make sure all processes are synchronized before continuing
>        MPI_Barrier(cr->mpi_comm_mygroup);
>
>(3) In mdlib/domdec.c, modify dd_distribute_vec to have external scope:
>
>//static void dd_distribute_vec(gmx_domdec_t *dd,t_block *cgs,rvec *v,rvec *lv)
>void dd_distribute_vec(gmx_domdec_t *dd,t_block *cgs,rvec *v,rvec *lv) // allow external functions access
>
>(4) In include/domdec.h, expose dd_distribute_vec for use by other functions:
>
>void dd_distribute_vec(gmx_domdec_t *dd,t_block *cgs,rvec *v,rvec *lv);
>
>----
>
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