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 = 3.52 3.52 3.52 Created orthogonal box = (0 -63.3635 0) to (44.8023 63.3635 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.08426 5.86667 4.97803 Created 1299 atoms create_atoms CPU = 0.00101113 secs 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.08426 5.86667 4.97803 Created 1299 atoms create_atoms CPU = 0.000905991 secs 1299 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 14 38 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 2583 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 14 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.126 | 6.126 | 6.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11279.293 0 -11279.293 227834.41 30 0 -11475.9 0 -11475.9 18292.321 Loop time of 2.46433 on 1 procs for 30 steps with 2583 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11279.293403 -11475.8959148 -11475.8996009 Force two-norm initial, final = 37179.4 174.813 Force max component initial, final = 10627.9 38.0728 Final line search alpha, max atom move = 2.59604e-07 9.88384e-06 Iterations, force evaluations = 30 427 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.415 | 2.415 | 2.415 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.031259 | 0.031259 | 0.031259 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01808 | | | 0.73 Nlocal: 2583 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381 ave 11381 max 11381 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: 343606 ave 343606 max 343606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343606 Ave neighs/atom = 133.026 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.126 | 6.126 | 6.126 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -11475.9 0 -11475.9 18292.321 28263.577 31 0 -11475.9 0 -11475.9 -29640.302 28263.625 Loop time of 0.0677099 on 1 procs for 1 steps with 2583 atoms 88.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11475.8996009 -11475.8996009 -11475.8996955 Force two-norm initial, final = 202.152 852.381 Force max component initial, final = 98.0318 754.877 Final line search alpha, max atom move = 3.18774e-07 0.000240635 Iterations, force evaluations = 1 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.064668 | 0.064668 | 0.064668 | 0.0 | 95.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071836 | 0.00071836 | 0.00071836 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002324 | | | 3.43 Nlocal: 2583 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381 ave 11381 max 11381 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: 343310 ave 343310 max 343310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343310 Ave neighs/atom = 132.911 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 14 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.264 | 6.264 | 6.264 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11475.9 0 -11475.9 -29640.302 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2583 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 | | 1.907e-06 | | |100.00 Nlocal: 2583 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381 ave 11381 max 11381 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: 343310 ave 343310 max 343310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343310 Ave neighs/atom = 132.911 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) = 6.264 | 6.264 | 6.264 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 -11475.9 -11475.9 44.802302 126.72704 4.9780384 -29640.302 -29640.302 -42791.64 -27361.347 -18767.92 2.177147 1009.0254 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2583 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: 2583 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381 ave 11381 max 11381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171655 ave 171655 max 171655 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343310 ave 343310 max 343310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343310 Ave neighs/atom = 132.911 Neighbor list builds = 0 Dangerous builds = 0 2583 -11475.899695512 eV 2.17714696115374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02