<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Dear All,<br>I need to hack mdrun in rather complex way and need some help from people, who understand Gromacs internals really well.<br>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.<br>Here is my additional code in md.c so far:<br><br>...<br>/* ######## END FIRST UPDATE STEP ############## */<br>/* ######## If doing VV, we now have v(dt)
###### */<br> <br> /* ################## START TRAJECTORY OUTPUT ################# */<br><br>/* Some preparations goes here */<br>...<br>/* Collecting data*/<br>if (DOMAINDECOMP(cr))<br> {<br> /*We need to collect x and f only*/<br> dd_collect_vec(cr->dd,state_local,state_local->x,state_global->x);<br> dd_collect_vec(cr->dd,state_local,f_local,f_global);<br> }<br><br>if (MASTER(cr))<br> {<br> printf("Collected %d atoms at step: %d\n",top_global->natoms,step);<br> /* Actually pass data */<br> pass_to(top_global->natoms, t, state_global->x, f_global);<br>
...<br> /* Processing data here */<br> ...<br> /* Get data back */<br> pass_from(state_global->x, f_global);<br> }<br>...<br>if (DOMAINDECOMP(cr)){<br> /* Here I have to redistribute it back and I'm totally stuck :( */<br>}<br><br>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. <br>Any hints are deeply appreciated!<br><br>Regards,<br>Semen<br></div></body></html>