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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -45.178384 0.0000000) to (27.665997 45.178384 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4622576 4.3721016 4.6847802 Created 744 atoms using lattice units in orthogonal box = (0.0000000 -45.178384 0.0000000) to (27.665997 45.178384 7.0271702) create_atoms CPU = 0.002 seconds 744 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4622576 4.3721016 4.6847802 Created 750 atoms using lattice units in orthogonal box = (0.0000000 -45.178384 0.0000000) to (27.665997 45.178384 7.0271702) create_atoms CPU = 0.001 seconds 750 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 = 6 18 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1482 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 = 6 18 2 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) = 6.778 | 6.778 | 6.778 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5719.3868 0 -5719.3868 41208.312 91 0 -6095.2918 0 -6095.2918 -1667.0756 Loop time of 3.39987 on 1 procs for 91 steps with 1482 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5719.38676560484 -6095.28596788503 -6095.29181810809 Force two-norm initial, final = 420.09040 0.32159477 Force max component initial, final = 75.458853 0.039736011 Final line search alpha, max atom move = 1.0000000 0.039736011 Iterations, force evaluations = 91 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2738 | 3.2738 | 3.2738 | 0.0 | 96.29 Neigh | 0.092749 | 0.092749 | 0.092749 | 0.0 | 2.73 Comm | 0.019599 | 0.019599 | 0.019599 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.40 Nlocal: 1482.00 ave 1482 max 1482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11202.0 ave 11202 max 11202 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: 572820.0 ave 572820 max 572820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 572820 Ave neighs/atom = 386.51822 Neighbor list builds = 3 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 = 6 18 2 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.778 | 6.778 | 6.778 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -6095.2918 0 -6095.2918 -1667.0756 17566.591 96 0 -6095.5733 0 -6095.5733 26.228149 17548.5 Loop time of 0.151045 on 1 procs for 5 steps with 1482 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 = -6095.29181810809 -6095.57250567233 -6095.57334007708 Force two-norm initial, final = 115.52387 1.1371326 Force max component initial, final = 106.60622 0.81271889 Final line search alpha, max atom move = 0.00022035404 0.00017908589 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14761 | 0.14761 | 0.14761 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062654 | 0.00062654 | 0.00062654 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002804 | | | 1.86 Nlocal: 1482.00 ave 1482 max 1482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11178.0 ave 11178 max 11178 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: 571872.0 ave 571872 max 571872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 571872 Ave neighs/atom = 385.87854 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 = 6 18 2 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) = 6.916 | 6.916 | 6.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6095.5733 0 -6095.5733 26.228149 Loop time of 2.359e-06 on 1 procs for 0 steps with 1482 atoms 169.6% 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 | | 2.359e-06 | | |100.00 Nlocal: 1482.00 ave 1482 max 1482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11190.0 ave 11190 max 11190 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: 574872.0 ave 574872 max 574872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574872 Ave neighs/atom = 387.90283 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 = 6 18 2 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) = 6.916 | 6.916 | 6.916 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 -6095.5733 -6095.5733 27.553301 90.613224 7.0286965 26.228149 26.228149 -32.277197 36.744365 74.217278 2.3228927 1428.9042 Loop time of 2.592e-06 on 1 procs for 0 steps with 1482 atoms 270.1% 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 | | 2.592e-06 | | |100.00 Nlocal: 1482.00 ave 1482 max 1482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11190.0 ave 11190 max 11190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287436.0 ave 287436 max 287436 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 574872.0 ave 574872 max 574872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574872 Ave neighs/atom = 387.90283 Neighbor list builds = 0 Dangerous builds = 0 1482 -6095.57334007708 eV 2.32289267286419 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04