LAMMPS (5 Oct 2016) # Exercise different output data options variable len equal 4.0 variable lenz equal 10.0 dimension 2 units metal boundary f f p lattice hex 1.0 origin 0.25 0.25 0.0 Lattice spacing in x,y,z = 1 1.73205 1 atom_style atomic region box block 0 ${len} 0 ${len} 0.0 ${lenz} region box block 0 4 0 ${len} 0.0 ${lenz} region box block 0 4 0 4 0.0 ${lenz} region box block 0 4 0 4 0.0 10 region atoms block 0 ${len} 0 ${len} 0.0 0.0 region atoms block 0 4 0 ${len} 0.0 0.0 region atoms block 0 4 0 4 0.0 0.0 create_box 1 box Created orthogonal box = (0 0 0) to (4 6.9282 10) 1 by 1 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms mass 1 1.0 pair_style lj/cut 2.5 pair_coeff 1 1 0.0 1.0 neighbor 1.0 nsq # # TEST 1: # # This compute voronoi generates all three # types of quantity: per-atom, local, and global compute v1 all voronoi/atom neighbors yes edge_histo 6 # write voronoi per-atom quantities to a file dump dperatom all custom 1 dump.voro id type x y z c_v1[1] c_v1[2] # writing voronoi local quantities to a file dump dlocal all local 1 dump.neighbors index c_v1[1] c_v1[2] c_v1[3] # sum up a voronoi per-atom quantity compute volvor all reduce sum c_v1[1] variable volsys equal lz*lx*ly variable err equal c_volvor-v_volsys # output voronoi global quantities thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] thermo 1 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.5 ghost atom cutoff = 3.5 Memory usage per processor = 9.40674 Mbytes c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0 Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325 Ave neighs/atom = 10.1562 Neighbor list builds = 0 Dangerous builds = 0 uncompute v1 uncompute volvor undump dperatom undump dlocal # # TEST 2: # # This compute voronoi generates # local and global quantities, but # not per-atom quantities compute v2 all voronoi/atom neighbors yes edge_histo 6 peratom no # write voronoi local quantities to a file dump d2 all local 1 dump.neighbors2 index c_v2[1] c_v2[2] c_v2[3] # sum up a voronoi local quantity compute sumarea all reduce sum c_v2[3] # output voronoi global quantities thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] thermo 1 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Memory usage per processor = 8.15503 Mbytes c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] 1215.0706 0 186 12 36 0 Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325 ave 325 max 325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 325 Ave neighs/atom = 10.1562 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00