LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems variable rcut equal 10.0 variable rskin equal 2.0 variable rcomm equal 20.0 variable len equal 4.0 variable lenz equal 10.0 dimension 2 units metal boundary p p p #lattice sq 1.0 origin 0.5 0.5 0.0 lattice hex 1.0 origin 0.5 0.5 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) 2 by 2 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms Time spent = 0.000319481 secs mass 1 1.0 pair_style lj/cut ${rcut} pair_style lj/cut 10 pair_coeff 1 1 0.0 1.0 neighbor ${rskin} nsq neighbor 2 nsq # set the minimum communication cut-off comm_modify cutoff ${rcomm} comm_modify cutoff 20 compute v1 all voronoi/atom neighbors yes compute volvor all reduce sum c_v1[1] variable volsys equal lz*lx*ly variable err equal c_volvor-v_volsys thermo_style custom c_volvor v_volsys vol v_err thermo 1 # # TEST 1: Volume check for 2d bulk system # run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/nsq/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 5.1159077e-13 Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms 51.9% CPU use with 4 MPI tasks x 1 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 | | 2.795e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 2159 ave 2159 max 2159 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 2064 ave 2077 max 2051 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 8256 Ave neighs/atom = 258 Neighbor list builds = 0 Dangerous builds = 0 # # TEST 2: Volume check for 2d finite system # add margins in x and y directions # change_box all boundary f f p run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 3.4106051e-13 Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms 47.6% CPU use with 4 MPI tasks x 1 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 | | 1.889e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 24 ave 24 max 24 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 124 ave 124 max 124 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496 Ave neighs/atom = 15.5 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00