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 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.
Any hints are deeply appreciated!
Regards,
Semen
--
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
