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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -43.890167 0.0000000) to (35.836171 43.890167 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1194531 5.0757336 5.9114352 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.890167 0.0000000) to (35.836171 43.890167 8.8671528) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1194531 5.0757336 5.9114352 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.890167 0.0000000) to (35.836171 43.890167 8.8671528) 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 ghost atom cutoff = 6 binsize = 3, bins = 12 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 24 atoms, new total = 2336 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_227887284491_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 = 12 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7474.5865 0 -7474.5865 104824.29 85 0 -8231.7663 0 -8231.7663 -1824.6203 Loop time of 12.1797 on 1 procs for 85 steps with 2336 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 = -7474.58653510771 -8231.75849533874 -8231.76633439566 Force two-norm initial, final = 1437.4854 0.30477515 Force max component initial, final = 229.96976 0.051320353 Final line search alpha, max atom move = 1.0000000 0.051320353 Iterations, force evaluations = 85 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.115 | 12.115 | 12.115 | 0.0 | 99.47 Neigh | 0.028492 | 0.028492 | 0.028492 | 0.0 | 0.23 Comm | 0.01408 | 0.01408 | 0.01408 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02209 | | | 0.18 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6088.00 ave 6088 max 6088 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: 180560.0 ave 180560 max 180560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180560 Ave neighs/atom = 77.294521 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 ghost atom cutoff = 6 binsize = 3, bins = 12 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -8231.7663 0 -8231.7663 -1824.6203 27893.501 88 0 -8231.8129 0 -8231.8129 -5.6652756 27857.663 Loop time of 0.53166 on 1 procs for 3 steps with 2336 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8231.76633439564 -8231.81241514771 -8231.81287645553 Force two-norm initial, final = 64.163819 0.41855524 Force max component initial, final = 55.344976 0.12149274 Final line search alpha, max atom move = 0.00031012569 3.7678021e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52844 | 0.52844 | 0.52844 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076904 | 0.00076904 | 0.00076904 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002448 | | | 0.46 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5955.00 ave 5955 max 5955 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: 180608.0 ave 180608 max 180608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180608 Ave neighs/atom = 77.315068 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 = 12 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) = 5.239 | 5.239 | 5.239 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8231.8129 0 -8231.8129 -5.6652756 Loop time of 2.494e-06 on 1 procs for 0 steps with 2336 atoms 160.4% 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 | | 2.494e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5955.00 ave 5955 max 5955 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: 180608.0 ave 180608 max 180608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180608 Ave neighs/atom = 77.315068 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 = 12 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) = 5.239 | 5.239 | 5.239 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 -8231.8129 -8231.8129 35.812741 87.850783 8.8544479 -5.6652756 -5.6652756 -4.4381782 -5.5802537 -6.977395 2.2915889 1428.8787 Loop time of 1.0667e-05 on 1 procs for 0 steps with 2336 atoms 168.7% 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 | | 1.067e-05 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5955.00 ave 5955 max 5955 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90304.0 ave 90304 max 90304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180608.0 ave 180608 max 180608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180608 Ave neighs/atom = 77.315068 Neighbor list builds = 0 Dangerous builds = 0 2336 -8231.81287645553 eV 2.29158893942884 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13