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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748052 43.782243 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1068645 5.0632526 5.8968992 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748052 43.782243 8.8453488) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1068645 5.0632526 5.8968992 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748052 43.782243 8.8453488) create_atoms CPU = 0.001 seconds 1184 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.968 | 5.968 | 5.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8669.7145 0 -8669.7145 91371.603 51 0 -9944.3239 0 -9944.3239 8349.0413 Loop time of 12.6352 on 1 procs for 51 steps with 2352 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 = -8669.71445706769 -9944.31534697574 -9944.32393426319 Force two-norm initial, final = 1241.8181 0.42004576 Force max component initial, final = 166.59808 0.077128092 Final line search alpha, max atom move = 1.0000000 0.077128092 Iterations, force evaluations = 51 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.574 | 12.574 | 12.574 | 0.0 | 99.52 Neigh | 0.041458 | 0.041458 | 0.041458 | 0.0 | 0.33 Comm | 0.0078916 | 0.0078916 | 0.0078916 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01142 | | | 0.09 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7278.00 ave 7278 max 7278 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: 297840.0 ave 297840 max 297840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297840 Ave neighs/atom = 126.63265 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.968 | 5.968 | 5.968 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -9944.3239 0 -9944.3239 8349.0413 27688.24 58 0 -9945.1344 0 -9945.1344 363.86151 27815.787 Loop time of 1.35489 on 1 procs for 7 steps with 2352 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 = -9944.32393426321 -9945.12638862462 -9945.1344306703 Force two-norm initial, final = 287.15760 11.610768 Force max component initial, final = 249.09601 9.4543815 Final line search alpha, max atom move = 6.4527685e-05 0.00061006936 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3506 | 1.3506 | 1.3506 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056412 | 0.00056412 | 0.00056412 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003753 | | | 0.28 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7241.00 ave 7241 max 7241 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: 297824.0 ave 297824 max 297824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297824 Ave neighs/atom = 126.62585 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9945.1344 0 -9945.1344 363.86151 Loop time of 2.578e-06 on 1 procs for 0 steps with 2352 atoms 155.2% 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 | | 2.578e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 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: 294480.0 ave 294480 max 294480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294480 Ave neighs/atom = 125.20408 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.106 | 6.106 | 6.106 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 -9945.1344 -9945.1344 35.624463 87.744653 8.8986137 363.86151 363.86151 282.14111 545.68849 263.75493 2.2215506 2120.7837 Loop time of 2.568e-06 on 1 procs for 0 steps with 2352 atoms 272.6% 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 | | 2.568e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147240.0 ave 147240 max 147240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 294480.0 ave 294480 max 294480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294480 Ave neighs/atom = 125.20408 Neighbor list builds = 0 Dangerous builds = 0 2352 -9945.1344306703 eV 2.22155057987739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14