LAMMPS (24 Dec 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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -38.413686 0.0000000) to (38.410072 38.413686 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0986822 5.0986822 3.6133157 Created 454 atoms create_atoms CPU = 0.000 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0986822 5.0986822 3.6133157 Created 454 atoms create_atoms CPU = 0.000 seconds 454 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 20 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 900 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3113.3598 0 -3113.3598 23215.146 106 0 -3178.0824 0 -3178.0824 -2224.1629 Loop time of 5.68376 on 1 procs for 106 steps with 900 atoms 88.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3113.35983813601 -3178.07928088009 -3178.08240346212 Force two-norm initial, final = 54.095090 0.16053743 Force max component initial, final = 12.892131 0.035829946 Final line search alpha, max atom move = 1.0000000 0.035829946 Iterations, force evaluations = 106 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6668 | 5.6668 | 5.6668 | 0.0 | 99.70 Neigh | 0.0044292 | 0.0044292 | 0.0044292 | 0.0 | 0.08 Comm | 0.0077156 | 0.0077156 | 0.0077156 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004835 | | | 0.09 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6765.00 ave 6765 max 6765 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161012.0 ave 161012 max 161012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161012 Ave neighs/atom = 178.90222 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -3178.0824 0 -3178.0824 -2224.1629 10662.695 108 0 -3178.0935 0 -3178.0935 -288.52806 10648.015 Loop time of 0.146122 on 1 procs for 2 steps with 900 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 = -3178.08240346212 -3178.09342576267 -3178.09348704938 Force two-norm initial, final = 21.935146 0.16295247 Force max component initial, final = 17.646080 0.033629034 Final line search alpha, max atom move = 0.0016911178 5.6870659e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14526 | 0.14526 | 0.14526 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001996 | 0.0001996 | 0.0001996 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006582 | | | 0.45 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6770.00 ave 6770 max 6770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160828.0 ave 160828 max 160828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160828 Ave neighs/atom = 178.69778 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3178.0935 0 -3178.0935 -288.52806 Loop time of 2.20002e-06 on 1 procs for 0 steps with 900 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6770.00 ave 6770 max 6770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161018.0 ave 161018 max 161018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161018 Ave neighs/atom = 178.90889 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) = 5.132 | 5.132 | 5.132 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 -3178.0935 -3178.0935 38.375393 76.827372 3.6116017 -288.52806 -288.52806 0.86156422 -861.38809 -5.0576647 2.3075715 153.06976 Loop time of 2.59979e-06 on 1 procs for 0 steps with 900 atoms 153.9% 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 | | 2.6e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6770.00 ave 6770 max 6770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80509.0 ave 80509 max 80509 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161018.0 ave 161018 max 161018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161018 Ave neighs/atom = 178.90889 Neighbor list builds = 0 Dangerous builds = 0 900 -3178.09348704938 eV 2.30757145316207 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06