LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -39.8678 0) to (8.13725 39.8678 8.91391) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88235 5.31523 5.9426 Created 242 atoms create_atoms CPU = 0.000306845 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88235 5.31523 5.9426 Created 241 atoms create_atoms CPU = 0.000208855 secs 241 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 472 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1535.7267 0 -1535.7267 -5993.9391 62 0 -1541.1539 0 -1541.1539 -14141.916 Loop time of 0.401485 on 1 procs for 62 steps with 472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1535.72665548 -1541.15260913 -1541.15391706 Force two-norm initial, final = 5.09098 0.0972131 Force max component initial, final = 1.06872 0.00874909 Final line search alpha, max atom move = 1 0.00874909 Iterations, force evaluations = 62 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39606 | 0.39606 | 0.39606 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038643 | 0.0038643 | 0.0038643 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001558 | | | 0.39 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5617 ave 5617 max 5617 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: 147956 ave 147956 max 147956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147956 Ave neighs/atom = 313.466 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1541.1539 0 -1541.1539 -14141.916 5783.6014 68 0 -1541.3878 0 -1541.3878 -1160.7169 5732.6311 Loop time of 0.0402188 on 1 procs for 6 steps with 472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1541.15391706 -1541.38732067 -1541.38777394 Force two-norm initial, final = 74.1083 0.184066 Force max component initial, final = 54.1937 0.0372394 Final line search alpha, max atom move = 0.000607648 2.26284e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039002 | 0.039002 | 0.039002 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031495 | 0.00031495 | 0.00031495 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009019 | | | 2.24 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5608 ave 5608 max 5608 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: 148888 ave 148888 max 148888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148888 Ave neighs/atom = 315.441 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.166 | 5.166 | 5.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1541.3878 0 -1541.3878 -1160.7169 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 atoms 209.7% 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636 ave 5636 max 5636 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: 148980 ave 148980 max 148980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148980 Ave neighs/atom = 315.636 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) = 5.166 | 5.166 | 5.166 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 -1541.3878 -1541.3878 8.095255 79.735689 8.8811809 -1160.7169 -1160.7169 5.3162665 -3485.3347 -2.1323808 2.2496885 295.39481 Loop time of 1.90735e-06 on 1 procs for 0 steps with 472 atoms 209.7% 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636 ave 5636 max 5636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74490 ave 74490 max 74490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 148980 ave 148980 max 148980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148980 Ave neighs/atom = 315.636 Neighbor list builds = 0 Dangerous builds = 0 472 -1541.38777394003 eV 2.24968846755513 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00