LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.70048 3.70048 3.70048 Created orthogonal box = (0 -68.2371 0) to (34.1167 68.2371 3.70048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.21785 5.21785 3.70048 Created 682 atoms create_atoms CPU = 0.000238895 secs 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.21785 5.21785 3.70048 Created 682 atoms create_atoms CPU = 0.000247002 secs 682 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 35 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1348 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5333.542 0 -5333.542 5613.7801 366 0 -5395.4144 0 -5395.4144 -21190.22 Loop time of 3.71592 on 1 procs for 366 steps with 1348 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5333.54199857 -5395.4092132 -5395.41442866 Force two-norm initial, final = 79.0203 0.239609 Force max component initial, final = 19.2242 0.0177371 Final line search alpha, max atom move = 1 0.0177371 Iterations, force evaluations = 366 707 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6097 | 3.6097 | 3.6097 | 0.0 | 97.14 Neigh | 0.037704 | 0.037704 | 0.037704 | 0.0 | 1.01 Comm | 0.045882 | 0.045882 | 0.045882 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02262 | | | 0.61 Nlocal: 1348 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10672 ave 10672 max 10672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199220 ave 199220 max 199220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199220 Ave neighs/atom = 147.789 Neighbor list builds = 7 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 366 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.506 | 5.506 | 5.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 366 0 -5395.4144 0 -5395.4144 -21190.22 17229.596 399 0 -5408.3434 0 -5408.3434 -13563.165 17153.66 Loop time of 0.2253 on 1 procs for 33 steps with 1348 atoms 102.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5395.41442866 -5408.34325875 -5408.3434406 Force two-norm initial, final = 561.843 1.90781 Force max component initial, final = 474.285 0.781074 Final line search alpha, max atom move = 0.000427558 0.000333955 Iterations, force evaluations = 33 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20889 | 0.20889 | 0.20889 | 0.0 | 92.71 Neigh | 0.006227 | 0.006227 | 0.006227 | 0.0 | 2.76 Comm | 0.002466 | 0.002466 | 0.002466 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007721 | | | 3.43 Nlocal: 1348 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10757 ave 10757 max 10757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205172 ave 205172 max 205172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205172 Ave neighs/atom = 152.205 Neighbor list builds = 1 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.644 | 5.644 | 5.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5408.3434 0 -5408.3434 -13563.165 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1348 atoms 0.0% CPU use with 1 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 | | 1.192e-06 | | |100.00 Nlocal: 1348 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10757 ave 10757 max 10757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205144 ave 205144 max 205144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205144 Ave neighs/atom = 152.184 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.644 | 5.644 | 5.644 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -5408.3434 -5408.3434 33.099456 136.4742 3.7973917 -13563.165 -13563.165 -64.360686 -40550.269 -74.864092 2.3390863 236.50194 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1348 atoms 0.0% CPU use with 1 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 | | 1.192e-06 | | |100.00 Nlocal: 1348 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10757 ave 10757 max 10757 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102572 ave 102572 max 102572 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205144 ave 205144 max 205144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205144 Ave neighs/atom = 152.184 Neighbor list builds = 0 Dangerous builds = 0 1348 -5408.34344060401 eV 2.33908634552033 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04