[gmx-developers] Help needed with hacking mdrun

[Semen Esilevsky]

Dear All,
I need to hack mdrun in rather complex way and need some help from people, who 
understand Gromacs internals really well.
My  problem is the following. Each N MD steps I want to pass current  
coordinates and forces to custom function, which transforms them in a  certain 
way (doesn't matter how at this point). Then I want to pass  modified forces and 

coordinates back and continue simulation. Currently I  got stuck with domain 
decomposition stuff. I figured out how to collect  data on master node and pass 
it to my function. However,  I have no  idea how to distribute it back to all 
nodes correctly after  modification.
Here is my additional code in md.c  so far:

...
/* ########  END FIRST UPDATE STEP  ############## */
/* ########  If doing VV, we now have v(dt)  ###### */
        
 /* ################## START TRAJECTORY OUTPUT ################# */

/* Some preparations goes here */
...
/* Collecting data*/
if (DOMAINDECOMP(cr))
    {
        /*We need to collect x and f only*/
        dd_collect_vec(cr->dd,state_local,state_local->x,state_global->x);
        dd_collect_vec(cr->dd,state_local,f_local,f_global);
    }

if (MASTER(cr))
    {
        printf("Collected %d atoms at step: %d\n",top_global->natoms,step);
        /* Actually pass data */
        pass_to(top_global->natoms, t, state_global->x, f_global);
         ...
        /* Processing data here */
        ...
       /*  Get data back */
       pass_from(state_global->x, f_global);
    }
...
if (DOMAINDECOMP(cr)){
    /* Here I have to redistribute it back from state_global->x and I'm totally 
stuck :(  */
}

The problem is that functions like dd_distribute_vector(...) are only used  
deep inside domain decomposition code and they use some data structures, which 
are not exposed in .h files. 

Is there any other more elegant way of plugging custom code to mdrun?

Any hints are deeply appreciated!

Regards,
Semen