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 = 3.61358 3.61358 3.61358 Created orthogonal box = (0 -41.8338 0) to (29.5784 41.8338 5.11037) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7391 6.24332 5.11037 Created 538 atoms create_atoms CPU = 0.000650167 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7391 6.24332 5.11037 Created 538 atoms create_atoms CPU = 0.000452995 secs 538 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 8 23 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1064 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3732.5481 0 -3732.5481 6701.991 70 0 -3759.5367 0 -3759.5367 -8072.3363 Loop time of 0.309485 on 1 procs for 70 steps with 1064 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 = -3732.54812697 -3759.53332526 -3759.53665724 Force two-norm initial, final = 38.9278 0.171023 Force max component initial, final = 11.2554 0.0205182 Final line search alpha, max atom move = 1 0.0205182 Iterations, force evaluations = 70 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29598 | 0.29598 | 0.29598 | 0.0 | 95.64 Neigh | 0.0069158 | 0.0069158 | 0.0069158 | 0.0 | 2.23 Comm | 0.0037982 | 0.0037982 | 0.0037982 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002791 | | | 0.90 Nlocal: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6000 ave 6000 max 6000 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: 150000 ave 150000 max 150000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150000 Ave neighs/atom = 140.977 Neighbor list builds = 2 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3759.5367 0 -3759.5367 -8072.3363 12646.943 76 0 -3759.782 0 -3759.782 -905.13303 12581.111 Loop time of 0.0295041 on 1 procs for 6 steps with 1064 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 = -3759.53665724 -3759.78035721 -3759.78199132 Force two-norm initial, final = 101.665 3.62156 Force max component initial, final = 90.8895 3.43516 Final line search alpha, max atom move = 0.000164261 0.000564264 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028269 | 0.028269 | 0.028269 | 0.0 | 95.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009561 | | | 3.24 Nlocal: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 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: 150060 ave 150060 max 150060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150060 Ave neighs/atom = 141.034 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3759.782 0 -3759.782 -905.13303 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1064 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: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 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: 150312 ave 150312 max 150312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150312 Ave neighs/atom = 141.271 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) = 5.155 | 5.155 | 5.155 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 -3759.782 -3759.782 29.425895 83.667667 5.1101268 -905.13303 -905.13303 -435.20411 -2136.4229 -143.7721 2.3765206 615.42446 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1064 atoms 104.9% 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 | | 1.907e-06 | | |100.00 Nlocal: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6008 ave 6008 max 6008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75156 ave 75156 max 75156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 150312 ave 150312 max 150312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150312 Ave neighs/atom = 141.271 Neighbor list builds = 0 Dangerous builds = 0 1064 -3759.78731131608 eV 2.37652061927265 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00