LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -51.576123 0.0000000) to (36.469826 51.576123 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7207571 4.5508344 5.1067972 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.576123 0.0000000) to (36.469826 51.576123 5.1067972) create_atoms CPU = 0.002 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7207571 4.5508344 5.1067972 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.576123 0.0000000) to (36.469826 51.576123 5.1067972) create_atoms CPU = 0.001 seconds 821 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1634 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_984358344196_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 7.189 | 7.189 | 7.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6241.4392 0 -6241.4392 62444.741 316 0 -6762.2395 0 -6762.2395 7260.258 Loop time of 15.911 on 1 procs for 316 steps with 1634 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6241.43920500365 -6762.2329744533 -6762.23948021117 Force two-norm initial, final = 474.48017 0.35712805 Force max component initial, final = 85.971969 0.044028179 Final line search alpha, max atom move = 1.0000000 0.044028179 Iterations, force evaluations = 316 589 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.42 | 15.42 | 15.42 | 0.0 | 96.92 Neigh | 0.3307 | 0.3307 | 0.3307 | 0.0 | 2.08 Comm | 0.099211 | 0.099211 | 0.099211 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06068 | | | 0.38 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14000.0 ave 14000 max 14000 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: 623156.0 ave 623156 max 623156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623156 Ave neighs/atom = 381.36842 Neighbor list builds = 10 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 316 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.185 | 7.185 | 7.185 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -6762.2395 0 -6762.2395 7260.258 19211.488 321 0 -6762.5514 0 -6762.5514 -439.7223 19297.261 Loop time of 0.175467 on 1 procs for 5 steps with 1634 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 = -6762.2394802111 -6762.545256336 -6762.55139450307 Force two-norm initial, final = 163.02939 11.912564 Force max component initial, final = 129.94834 8.7273156 Final line search alpha, max atom move = 4.5422891e-05 0.00039641991 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17175 | 0.17175 | 0.17175 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071999 | 0.00071999 | 0.00071999 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002997 | | | 1.71 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13913.0 ave 13913 max 13913 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: 622764.0 ave 622764 max 622764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622764 Ave neighs/atom = 381.12852 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.323 | 7.323 | 7.323 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6762.5514 0 -6762.5514 -439.7223 Loop time of 3.679e-06 on 1 procs for 0 steps with 1634 atoms 190.3% 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 | | 3.679e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13912.0 ave 13912 max 13912 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: 621690.0 ave 621690 max 621690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621690 Ave neighs/atom = 380.47124 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.323 | 7.323 | 7.323 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 -6762.5514 -6762.5514 36.442117 103.6284 5.1099101 -439.7223 -439.7223 -667.35193 73.221773 -725.03675 2.3879131 1227.5134 Loop time of 2.322e-06 on 1 procs for 0 steps with 1634 atoms 258.4% 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 | | 2.322e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13912.0 ave 13912 max 13912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310845.0 ave 310845 max 310845 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621690.0 ave 621690 max 621690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621690 Ave neighs/atom = 380.47124 Neighbor list builds = 0 Dangerous builds = 0 1634 -6762.55139450306 eV 2.38791309657898 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16