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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -53.395608 0.0000000) to (32.697998 53.395608 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9450906 6.0676827 6.5725450 Created 1041 atoms using lattice units in orthogonal box = (0.0000000 -53.395608 0.0000000) to (32.697998 53.395608 9.8588175) create_atoms CPU = 0.002 seconds 1041 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9450906 6.0676827 6.5725450 Created 1065 atoms using lattice units in orthogonal box = (0.0000000 -53.395608 0.0000000) to (32.697998 53.395608 9.8588175) create_atoms CPU = 0.001 seconds 1065 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2106 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_149316865608_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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.961 | 5.961 | 5.961 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5152.1213 0 -5152.1213 27408.899 201 0 -5564.3912 0 -5564.3912 127.32093 Loop time of 5.6334 on 1 procs for 201 steps with 2106 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5152.1213008651 -5564.38604210905 -5564.39123267916 Force two-norm initial, final = 276.16060 0.18336998 Force max component initial, final = 41.114295 0.030152542 Final line search alpha, max atom move = 1.0000000 0.030152542 Iterations, force evaluations = 201 326 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3501 | 5.3501 | 5.3501 | 0.0 | 94.97 Neigh | 0.21582 | 0.21582 | 0.21582 | 0.0 | 3.83 Comm | 0.028232 | 0.028232 | 0.028232 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03927 | | | 0.70 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7648.00 ave 7648 max 7648 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: 294344.0 ave 294344 max 294344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294344 Ave neighs/atom = 139.76448 Neighbor list builds = 10 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 201 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.961 | 5.961 | 5.961 Mbytes Step Temp E_pair E_mol TotEng Press Volume 201 0 -5564.3912 0 -5564.3912 127.32093 34425.6 204 0 -5564.4607 0 -5564.4607 -184.92858 34438.779 Loop time of 0.0811945 on 1 procs for 3 steps with 2106 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5564.39123267916 -5564.45638102652 -5564.46067242899 Force two-norm initial, final = 42.372966 7.1238255 Force max component initial, final = 36.738671 4.7573564 Final line search alpha, max atom move = 9.4513271e-05 0.00044963331 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079095 | 0.079095 | 0.079095 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031893 | 0.00031893 | 0.00031893 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00178 | | | 2.19 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7674.00 ave 7674 max 7674 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: 294316.0 ave 294316 max 294316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294316 Ave neighs/atom = 139.75119 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.098 | 6.098 | 6.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5564.4607 0 -5564.4607 -184.92858 Loop time of 2.641e-06 on 1 procs for 0 steps with 2106 atoms 189.3% 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 | | 2.641e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7674.00 ave 7674 max 7674 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: 294322.0 ave 294322 max 294322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294322 Ave neighs/atom = 139.75404 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.098 | 6.098 | 6.098 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 -5564.4607 -5564.4607 32.670226 107.08016 9.8443397 -184.92858 -184.92858 -217.06949 -116.71738 -220.99887 2.6329337 1095.8906 Loop time of 2.865e-06 on 1 procs for 0 steps with 2106 atoms 209.4% 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 | | 2.865e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7674.00 ave 7674 max 7674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147161.0 ave 147161 max 147161 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 294322.0 ave 294322 max 294322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294322 Ave neighs/atom = 139.75404 Neighbor list builds = 0 Dangerous builds = 0 2106 -5499.73431432955 eV 2.63293372554055 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06