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 -63.941948 0.0000000) to (36.916901 63.941948 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -63.941948 0.0000000) to (36.916901 63.941948 6.2700239) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.941948 0.0000000) to (36.916901 63.941948 6.2700239) create_atoms CPU = 0.002 seconds 1249 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 = 13 43 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 5 atoms, new total = 2489 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 = 13 43 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) = 5.306 | 5.306 | 5.306 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8401.8376 0 -8401.8376 51108.968 137 0 -8784.417 0 -8784.417 563.28595 Loop time of 21.202 on 1 procs for 137 steps with 2489 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 = -8401.83759645793 -8784.40846942862 -8784.41701879728 Force two-norm initial, final = 883.26317 0.27613943 Force max component initial, final = 498.23222 0.081725319 Final line search alpha, max atom move = 1.0000000 0.081725319 Iterations, force evaluations = 137 259 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.089 | 21.089 | 21.089 | 0.0 | 99.47 Neigh | 0.055017 | 0.055017 | 0.055017 | 0.0 | 0.26 Comm | 0.025326 | 0.025326 | 0.025326 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03237 | | | 0.15 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8329.00 ave 8329 max 8329 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: 192642.0 ave 192642 max 192642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192642 Ave neighs/atom = 77.397348 Neighbor list builds = 4 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 = 13 43 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 : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -8784.417 0 -8784.417 563.28595 29601.266 139 0 -8784.4532 0 -8784.4532 -3.0480519 29612.999 Loop time of 0.399054 on 1 procs for 2 steps with 2489 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 = -8784.41701879724 -8784.44937052869 -8784.45323157222 Force two-norm initial, final = 48.822871 0.53371671 Force max component initial, final = 29.924877 0.39280621 Final line search alpha, max atom move = 4.1096020e-05 1.6142772e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39707 | 0.39707 | 0.39707 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030282 | 0.00030282 | 0.00030282 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001684 | | | 0.42 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8335.00 ave 8335 max 8335 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: 192646.0 ave 192646 max 192646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192646 Ave neighs/atom = 77.398955 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 = 13 43 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) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8784.4532 0 -8784.4532 -3.0480519 Loop time of 2.134e-06 on 1 procs for 0 steps with 2489 atoms 187.4% 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 | | 2.134e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8335.00 ave 8335 max 8335 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: 192642.0 ave 192642 max 192642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192642 Ave neighs/atom = 77.397348 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 = 13 43 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) = 5.444 | 5.444 | 5.444 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 -8784.4532 -8784.4532 36.945969 127.97474 6.2631247 -3.0480519 -3.0480519 12.32972 -21.267416 -0.20645964 2.2897088 1036.8911 Loop time of 2.138e-06 on 1 procs for 0 steps with 2489 atoms 187.1% 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 | | 2.138e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8335.00 ave 8335 max 8335 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96321.0 ave 96321 max 96321 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192642.0 ave 192642 max 192642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192642 Ave neighs/atom = 77.397348 Neighbor list builds = 0 Dangerous builds = 0 2489 -8784.45323157222 eV 2.28970879709351 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22