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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -56.7687 0) to (28.3826 56.7687 3.52043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9299 3.9299 3.52043 Created 522 atoms create_atoms CPU = 0.000194073 secs 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9299 3.9299 3.52043 Created 522 atoms create_atoms CPU = 8.70228e-05 secs 522 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 2 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1036 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.6 | 4.6 | 4.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5941.5837 0 -5941.5837 5669.2639 19 0 -5973.371 0 -5973.371 -867.05315 Loop time of 5.98072 on 1 procs for 19 steps with 1036 atoms 73.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5941.58370428 -5973.3651351 -5973.37098073 Force two-norm initial, final = 34.1601 0.292956 Force max component initial, final = 7.03323 0.0633192 Final line search alpha, max atom move = 0.909839 0.0576103 Iterations, force evaluations = 19 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9789 | 5.9789 | 5.9789 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010092 | 0.0010092 | 0.0010092 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008299 | | | 0.01 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5440 ave 5440 max 5440 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: 80528 ave 80528 max 80528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80528 Ave neighs/atom = 77.7297 Neighbor list builds = 0 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.6 | 4.6 | 4.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -5973.371 0 -5973.371 -867.05315 11344.513 20 0 -5973.3742 0 -5973.3742 -461.11556 11342.207 Loop time of 0.476385 on 1 procs for 1 steps with 1036 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5973.37098073 -5973.37098073 -5973.37416626 Force two-norm initial, final = 7.54967 3.35115 Force max component initial, final = 6.16539 2.72435 Final line search alpha, max atom move = 0.000162196 0.000441879 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47596 | 0.47596 | 0.47596 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003242 | | | 0.07 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444 ave 5444 max 5444 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: 80432 ave 80432 max 80432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80432 Ave neighs/atom = 77.6371 Neighbor list builds = 0 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5973.3742 0 -5973.3742 -461.11556 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1036 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 | | 9.537e-07 | | |100.00 Nlocal: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444 ave 5444 max 5444 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: 80432 ave 80432 max 80432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80432 Ave neighs/atom = 77.6371 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) = 4.738 | 4.738 | 4.738 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 -5973.3742 -5973.3742 28.363043 113.53736 3.5221346 -461.11556 -461.11556 272.28059 -2040.6505 385.02328 2.1731657 257.68517 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1036 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: 1036 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5444 ave 5444 max 5444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40216 ave 40216 max 40216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80432 ave 80432 max 80432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80432 Ave neighs/atom = 77.6371 Neighbor list builds = 0 Dangerous builds = 0 1036 -2518.5198707049 eV 2.17316574660626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07