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 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) create_atoms CPU = 0.002 seconds 1080 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.009251 0.0000000) to (41.723293 59.009251 5.0973115) create_atoms CPU = 0.002 seconds 1080 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 = 14 40 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 48 atoms, new total = 2112 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 = 14 40 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8913.9102 0 -8913.9102 -7240.8798 459 0 -8981.6823 0 -8981.6823 -30507.172 Loop time of 126.34 on 1 procs for 459 steps with 2112 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 = -8913.91019248201 -8981.67366167808 -8981.68230052828 Force two-norm initial, final = 7.4125889 0.29457872 Force max component initial, final = 1.0578417 0.071304306 Final line search alpha, max atom move = 0.99754511 0.071129262 Iterations, force evaluations = 459 882 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 125.71 | 125.71 | 125.71 | 0.0 | 99.50 Neigh | 0.301 | 0.301 | 0.301 | 0.0 | 0.24 Comm | 0.16192 | 0.16192 | 0.16192 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1657 | | | 0.13 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7926.00 ave 7926 max 7926 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: 140188.0 ave 140188 max 140188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140188 Ave neighs/atom = 66.376894 Neighbor list builds = 14 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 = 14 40 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 : 459 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes Step Temp E_pair E_mol TotEng Press Volume 459 0 -8981.6823 0 -8981.6823 -30507.172 25099.776 481 0 -8995.375 0 -8995.375 15548.615 24373.966 Loop time of 3.67676 on 1 procs for 22 steps with 2112 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8981.68230052829 -8995.37353455399 -8995.37503925898 Force two-norm initial, final = 1204.8676 3.5627993 Force max component initial, final = 1024.0221 3.3259681 Final line search alpha, max atom move = 8.3695385e-05 0.00027836818 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6538 | 3.6538 | 3.6538 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0031968 | 0.0031968 | 0.0031968 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01977 | | | 0.54 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7917.00 ave 7917 max 7917 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: 140298.0 ave 140298 max 140298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140298 Ave neighs/atom = 66.428977 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 = 14 40 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) = 5.358 | 5.358 | 5.358 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8995.375 0 -8995.375 15548.615 Loop time of 3.729e-06 on 1 procs for 0 steps with 2112 atoms 160.9% 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 | | 3.729e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8076.00 ave 8076 max 8076 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: 142078.0 ave 142078 max 142078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142078 Ave neighs/atom = 67.271780 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 = 14 40 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) = 5.358 | 5.358 | 5.358 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 -8995.375 -8995.375 41.384884 118.0185 4.9903886 15548.615 15548.615 9.873606 46850.01 -214.04024 2.2617391 5659.5024 Loop time of 4.315e-06 on 1 procs for 0 steps with 2112 atoms 208.6% 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 | | 4.315e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8076.00 ave 8076 max 8076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71039.0 ave 71039 max 71039 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142078.0 ave 142078 max 142078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142078 Ave neighs/atom = 67.271780 Neighbor list builds = 0 Dangerous builds = 0 2112 -8995.37503925898 eV 2.2617391457204 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:10