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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -43.748919 0.0000000) to (53.576830 43.748919 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1375043 5.3932560 5.9120667 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.748919 0.0000000) to (53.576830 43.748919 8.8681001) create_atoms CPU = 0.002 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1375043 5.3932560 5.9120667 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.748919 0.0000000) to (53.576830 43.748919 8.8681001) create_atoms CPU = 0.002 seconds 1757 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 = 18 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 58 atoms, new total = 3456 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_390178379548_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 = 18 30 3 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) = 5.668 | 5.668 | 5.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12130.9 0 -12130.9 -869.89536 65 0 -12197.842 0 -12197.842 -14219.808 Loop time of 5.66863 on 1 procs for 65 steps with 3456 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 = -12130.8996594186 -12197.830684059 -12197.8421808993 Force two-norm initial, final = 52.836282 0.36630693 Force max component initial, final = 8.9006478 0.11229049 Final line search alpha, max atom move = 1.0000000 0.11229049 Iterations, force evaluations = 65 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6223 | 5.6223 | 5.6223 | 0.0 | 99.18 Neigh | 0.019949 | 0.019949 | 0.019949 | 0.0 | 0.35 Comm | 0.0096744 | 0.0096744 | 0.0096744 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0167 | | | 0.29 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8108.00 ave 8108 max 8108 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: 266420.0 ave 266420 max 266420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266420 Ave neighs/atom = 77.089120 Neighbor list builds = 1 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 = 18 30 3 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.668 | 5.668 | 5.668 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -12197.842 0 -12197.842 -14219.808 41572.384 70 0 -12199.29 0 -12199.29 -2464.9721 41221.983 Loop time of 0.351711 on 1 procs for 5 steps with 3456 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12197.8421808992 -12199.2784039143 -12199.2896536696 Force two-norm initial, final = 482.50407 6.7305045 Force max component initial, final = 345.90170 5.6802337 Final line search alpha, max atom move = 2.7785052e-05 0.00015782559 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34803 | 0.34803 | 0.34803 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046255 | 0.00046255 | 0.00046255 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003218 | | | 0.91 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8082.00 ave 8082 max 8082 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: 266640.0 ave 266640 max 266640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266640 Ave neighs/atom = 77.152778 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 = 18 30 3 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) = 5.806 | 5.806 | 5.806 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12199.29 0 -12199.29 -2464.9721 Loop time of 1.924e-06 on 1 procs for 0 steps with 3456 atoms 207.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 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: 266804.0 ave 266804 max 266804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266804 Ave neighs/atom = 77.200231 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 = 18 30 3 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) = 5.806 | 5.806 | 5.806 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 -12199.29 -12199.29 53.338173 87.497839 8.8326988 -2464.9721 -2464.9721 -137.6392 -7477.1697 219.89255 2.2969061 1577.1492 Loop time of 1.861e-06 on 1 procs for 0 steps with 3456 atoms 214.9% 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 | | 1.861e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133402.0 ave 133402 max 133402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266804.0 ave 266804 max 266804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266804 Ave neighs/atom = 77.200231 Neighbor list builds = 0 Dangerous builds = 0 3456 -12199.2896536696 eV 2.29690608084797 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06