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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0462295 6.2186617 5.0973115 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) create_atoms CPU = 0.003 seconds 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0462295 6.2186617 5.0973115 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) create_atoms CPU = 0.002 seconds 690 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 = 8 45 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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_492310898779_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 = 8 45 2 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5772.9248 0 -5772.9248 568.22063 137 0 -5801.6508 0 -5801.6508 -7697.1753 Loop time of 13.1198 on 1 procs for 137 steps with 1368 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 = -5772.92476202827 -5801.64612111968 -5801.65078549698 Force two-norm initial, final = 26.539230 0.19987373 Force max component initial, final = 7.9643430 0.050904836 Final line search alpha, max atom move = 1.0000000 0.050904836 Iterations, force evaluations = 137 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.054 | 13.054 | 13.054 | 0.0 | 99.50 Neigh | 0.025424 | 0.025424 | 0.025424 | 0.0 | 0.19 Comm | 0.020047 | 0.020047 | 0.020047 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02015 | | | 0.15 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5910.00 ave 5910 max 5910 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: 105856.0 ave 105856 max 105856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105856 Ave neighs/atom = 77.380117 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 45 2 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 : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -5801.6508 0 -5801.6508 -7697.1753 16108.696 139 0 -5801.7115 0 -5801.7115 -3664.0139 16068.124 Loop time of 0.190878 on 1 procs for 2 steps with 1368 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 = -5801.65078549698 -5801.70586895265 -5801.7114821234 Force two-norm initial, final = 67.354238 3.6460985 Force max component initial, final = 53.373497 3.2002527 Final line search alpha, max atom move = 5.6104222e-05 0.00017954769 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18965 | 0.18965 | 0.18965 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019975 | 0.00019975 | 0.00019975 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001025 | | | 0.54 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5900.00 ave 5900 max 5900 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: 106028.0 ave 106028 max 106028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106028 Ave neighs/atom = 77.505848 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 = 8 45 2 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5801.7115 0 -5801.7115 -3664.0139 Loop time of 1.822e-06 on 1 procs for 0 steps with 1368 atoms 219.5% 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 | | 1.822e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5920.00 ave 5920 max 5920 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: 106048.0 ave 106048 max 106048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106048 Ave neighs/atom = 77.520468 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 = 8 45 2 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) = 5.213 | 5.213 | 5.213 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 -5801.7115 -5801.7115 23.600029 133.70844 5.0920637 -3664.0139 -3664.0139 -172.75193 -11138.063 318.77344 2.3536974 542.42335 Loop time of 1.986e-06 on 1 procs for 0 steps with 1368 atoms 201.4% 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 | | 1.986e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5920.00 ave 5920 max 5920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53024.0 ave 53024 max 53024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106048.0 ave 106048 max 106048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106048 Ave neighs/atom = 77.520468 Neighbor list builds = 0 Dangerous builds = 0 1368 -5801.7114821234 eV 2.35369741965654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13