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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -63.952399 0.0000000) to (36.920845 63.952399 6.2706937) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6801300 5.7389930 6.2706937 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.952399 0.0000000) to (36.920845 63.952399 6.2706937) create_atoms CPU = 0.003 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6801300 5.7389930 6.2706937 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.952399 0.0000000) to (36.920845 63.952399 6.2706937) create_atoms CPU = 0.003 seconds 1251 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 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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_390178379548_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8713.9723 0 -8713.9723 3729.4597 34 0 -8752.4133 0 -8752.4133 -3663.2888 Loop time of 2.52499 on 1 procs for 34 steps with 2480 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 = -8713.97230212448 -8752.40457535832 -8752.41326731667 Force two-norm initial, final = 58.790639 0.28450744 Force max component initial, final = 10.084952 0.073950140 Final line search alpha, max atom move = 1.0000000 0.073950140 Iterations, force evaluations = 34 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5114 | 2.5114 | 2.5114 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057014 | 0.0057014 | 0.0057014 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007918 | | | 0.31 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8227.00 ave 8227 max 8227 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: 191814.0 ave 191814 max 191814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191814 Ave neighs/atom = 77.344355 Neighbor list builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.308 | 5.308 | 5.308 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -8752.4133 0 -8752.4133 -3663.2888 29612.431 36 0 -8752.4821 0 -8752.4821 -791.57111 29552.555 Loop time of 0.151931 on 1 procs for 2 steps with 2480 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 = -8752.41326731667 -8752.4746909509 -8752.48205693699 Force two-norm initial, final = 87.709758 9.2698690 Force max component initial, final = 79.826032 9.2642515 Final line search alpha, max atom move = 3.8116152e-05 0.00035311762 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15018 | 0.15018 | 0.15018 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025672 | 0.00025672 | 0.00025672 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001495 | | | 0.98 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8233.00 ave 8233 max 8233 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: 191896.0 ave 191896 max 191896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191896 Ave neighs/atom = 77.377419 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 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.446 | 5.446 | 5.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8752.4821 0 -8752.4821 -791.57111 Loop time of 2.316e-06 on 1 procs for 0 steps with 2480 atoms 172.7% 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 | | 2.316e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8233.00 ave 8233 max 8233 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: 191912.0 ave 191912 max 191912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191912 Ave neighs/atom = 77.383871 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 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.446 | 5.446 | 5.446 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 -8752.4821 -8752.4821 36.903772 127.9048 6.2609097 -791.57111 -791.57111 502.02435 -2868.5393 -8.1983689 2.2859474 1086.7721 Loop time of 4.923e-06 on 1 procs for 0 steps with 2480 atoms 243.8% 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 | | 4.923e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8233.00 ave 8233 max 8233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95956.0 ave 95956 max 95956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191912.0 ave 191912 max 191912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191912 Ave neighs/atom = 77.383871 Neighbor list builds = 0 Dangerous builds = 0 2480 -8752.48205693699 eV 2.28594738222741 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03