[gmx-developers] neighbor list, Monte Carlo

[Jason DeJoannis]

Hi, 
 
Lets say we wish to add a Monte Carlo move into mdrun. 
It is simpler to consider only the class of fixed-topology moves. 
That is to say, only change the position of one or more atoms. 
This should be easy. Just have to make sure the neighbor list  
gets updated afterwards. 
 
Here is my first effort. I have added the following lines just 
before do_force() is called. 
 
      if (MASTER(cr)) 
        if (step%777 == 0) { 
          printf("\nYippie! JASON WAS HERE on Step %d\n\n",step); 
          do_swap(nsb->natoms,x); 
          bNS = TRUE; 
        } 
 
where do_swap() swaps the postion of two randomly selected atoms. 
I hacked it into md.c as follows: 
 
static void do_swap(int natom, rvec x[]) 
{ 
  static bool bFirst = TRUE; 
  static bool bDebug = TRUE; 
  static int swap_seed; 
  int i,j; 
  rvec temp; 
 
  if (bFirst) { 
    swap_seed = make_seed(); 
    if (bDebug) 
      printf("Initial do_swap seed: %d\n",swap_seed); 
    bFirst = FALSE; 
  } 
 
  i = (int)(natom*rando(&swap_seed)); 
  j = (int)(natom*rando(&swap_seed)); 
 
  if (bDebug) 
    printf("Swap atoms: %d %d\n",i,j); 
 
  copy_rvec(x[i],temp); 
  copy_rvec(x[j],x[i]); 
  copy_rvec(temp,x[j]); 
} 
 
By setting bNS = TRUE I am hoping to force a complete 
list regeneration immediately after the swap move. 
 
To test this I am using a Argon/Krypton mixture. It always 
works on one processor and it fails just after the swap about  
half the time on two processors. Here is a copy of the crash  
message. 
 
MPI_Wait: message truncated (rank 1, MPI_COMM_WORLD) 
Rank (1, MPI_COMM_WORLD): Call stack within LAM: 
Rank (1, MPI_COMM_WORLD):  - MPI_Wait() 
Rank (1, MPI_COMM_WORLD):  - main() 
----------------------------------------------------------------------------- 
 
One of the processes started by mpirun has exited with a nonzero exit 
code.  This typically indicates that the process finished in error. 
If your process did not finish in error, be sure to include a "return 
0" or "exit(0)" in your C code before exiting the application. 
 
PID 5095 failed on node n0 with exit status 1. 
----------------------------------------------------------------------------- 
make: *** [run] Error 1 
 
 
Maybe it crashes when the atoms are not in the same slab. 
Could someone describe the structure of the neighbor search 
routines to me. I have read everything in the manual about  
them.  
 
  Thanks, 
 
--- 
Jason de Joannis, Ph.D. 
Chemistry Department, Emory University 
1515 Pierce Dr. NE, Atlanta, GA 30322 
Phone: (404) 712-2983 
Email: jdejoan at emory.edu 
http://userwww.service.emory.edu/~jdejoan