Interpret Aspherix® screen output

Description

This text describes how to interpret the screen output of a simulation.

Detailed Description

As Aspherix® reads an input script, it prints information to both the screen and a log file about significant actions it takes to setup a simulation. When the simulation is ready to begin, Aspherix® performs various initializations and prints the amount of memory (in MBytes per processor) that the simulation requires. It also prints details of the initial thermodynamic state of the system. During the run itself, thermodynamic information is printed periodically, every few timesteps. When the run concludes, Aspherix® prints the final thermodynamic state and a total run time for the simulation. It then appends statistics about the CPU time and storage requirements for the simulation. An example set of statistics is shown here:

Loop time of 49.002 on 2 procs for 2004 atoms

Pair   time (%) = 35.0495 (71.5267)
Neigh  time (%) = 2.73485 (5.5811)
Comm   time (%) = 1.50291 (3.06703)
Outpt  time (%) = 0.013799 (0.0281601)
Other  time (%) = 2.13669 (4.36041)

Nlocal:    1002 ave, 1015 max, 989 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost:    8720 ave, 8724 max, 8716 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs:    354141 ave, 361422 max, 346860 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 708282
Ave neighs/atom = 353.434
Ave special neighs/atom = 2.34032
Number of reneighborings = 42
Dangerous reneighborings = 2

The first section gives the breakdown of the CPU run time (in seconds) into major categories. The second section lists the number of owned atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored per processor. The max and min values give the spread of these values across processors with a 10-bin histogram showing the distribution. The total number of histogram counts is equal to the number of processors.

The last section gives aggregate statistics for pair-wise neighbors. The number of times neighbor lists were rebuilt during the run is given as well as the number of potentially “dangerous” rebuilds. If atom movement triggered neighbor list rebuilding (see the neigh_modify command), then dangerous reneighborings are those that were triggered on the first timestep atom movement was checked for. If this count is non-zero you may wish to reduce the delay factor to ensure no force interactions are missed by atoms moving beyond the neighbor skin distance before a rebuild takes place.