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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -80.185909 0.0000000) to (49.103641 80.185909 9.9204335) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6786523 5.7275649 6.6136223 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -80.185909 0.0000000) to (49.103641 80.185909 9.9204335) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6786523 5.7275649 6.6136223 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.185909 0.0000000) to (49.103641 80.185909 9.9204335) create_atoms CPU = 0.003 seconds 2358 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 37 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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_664470114311_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15681.966 0 -15681.966 3168.7697 25 0 -15775.885 0 -15775.885 3192.4883 Loop time of 1.71805 on 1 procs for 25 steps with 4704 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15681.9660589223 -15775.8702450871 -15775.8851188009 Force two-norm initial, final = 52.405027 0.23679359 Force max component initial, final = 8.7440450 0.0097911680 Final line search alpha, max atom move = 1.0000000 0.0097911680 Iterations, force evaluations = 25 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6999 | 1.6999 | 1.6999 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068977 | 0.0068977 | 0.0068977 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01127 | | | 0.66 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14710.0 ave 14710 max 14710 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: 825660.0 ave 825660 max 825660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825660 Ave neighs/atom = 175.52296 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.29 | 12.29 | 12.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -15775.885 0 -15775.885 3192.4883 78121.828 32 0 -15776.787 0 -15776.787 19.523535 78432.369 Loop time of 0.387168 on 1 procs for 7 steps with 4704 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 = -15775.885118801 -15776.7801153428 -15776.7874516862 Force two-norm initial, final = 327.92468 1.7198430 Force max component initial, final = 308.04828 1.1844611 Final line search alpha, max atom move = 6.0760032e-05 7.1967893e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3332 | 0.3332 | 0.3332 | 0.0 | 86.06 Neigh | 0.046004 | 0.046004 | 0.046004 | 0.0 | 11.88 Comm | 0.0013762 | 0.0013762 | 0.0013762 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006591 | | | 1.70 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14679.0 ave 14679 max 14679 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: 819996.0 ave 819996 max 819996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 819996 Ave neighs/atom = 174.31888 Neighbor list builds = 1 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 11.80 | 11.80 | 11.80 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15776.787 0 -15776.787 19.523535 Loop time of 2.302e-06 on 1 procs for 0 steps with 4704 atoms 173.8% 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 | | 2.302e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14679.0 ave 14679 max 14679 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: 820032.0 ave 820032 max 820032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 820032 Ave neighs/atom = 174.32653 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 11.80 | 11.80 | 11.80 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 -15776.787 -15776.787 49.03952 161.42713 9.9076941 19.523535 19.523535 14.973549 19.432559 24.164497 2.5007703 2366.4026 Loop time of 2.691e-06 on 1 procs for 0 steps with 4704 atoms 297.3% 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 | | 2.691e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14679.0 ave 14679 max 14679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 410016.0 ave 410016 max 410016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 820032.0 ave 820032 max 820032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 820032 Ave neighs/atom = 174.32653 Neighbor list builds = 0 Dangerous builds = 0 4704 -15748.1898854305 eV 2.50077034058268 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02