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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -53.439379 0.0000000) to (43.633070 53.439379 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3794196 5.1243240 5.8968993 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -53.439379 0.0000000) to (43.633070 53.439379 8.8453489) create_atoms CPU = 0.003 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3794196 5.1243240 5.8968993 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -53.439379 0.0000000) to (43.633070 53.439379 8.8453489) create_atoms CPU = 0.002 seconds 1755 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 = 15 36 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 0 atoms, new total = 3502 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_321233176498_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 = 15 36 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) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14250.107 0 -14250.107 40495.532 118 0 -14809.723 0 -14809.723 5978.4943 Loop time of 43.9588 on 1 procs for 118 steps with 3502 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 = -14250.1066406403 -14809.712472882 -14809.7233349176 Force two-norm initial, final = 474.34100 0.39917568 Force max component initial, final = 91.426814 0.11860805 Final line search alpha, max atom move = 0.96030017 0.11389933 Iterations, force evaluations = 118 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.698 | 43.698 | 43.698 | 0.0 | 99.41 Neigh | 0.15668 | 0.15668 | 0.15668 | 0.0 | 0.36 Comm | 0.038267 | 0.038267 | 0.038267 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06601 | | | 0.15 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8102.00 ave 8102 max 8102 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: 270186.0 ave 270186 max 270186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270186 Ave neighs/atom = 77.151913 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 = 15 36 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 : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.640 | 5.640 | 5.640 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -14809.723 0 -14809.723 5978.4943 41249.827 122 0 -14810.085 0 -14810.085 -168.35964 41396.901 Loop time of 1.41083 on 1 procs for 4 steps with 3502 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 = -14809.7233349176 -14810.0841815052 -14810.0851123995 Force two-norm initial, final = 277.85731 8.7911877 Force max component initial, final = 211.15458 7.9474056 Final line search alpha, max atom move = 0.00011181527 0.00088864130 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.404 | 1.404 | 1.404 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008459 | 0.0008459 | 0.0008459 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005936 | | | 0.42 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8099.00 ave 8099 max 8099 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: 270016.0 ave 270016 max 270016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270016 Ave neighs/atom = 77.103370 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 = 15 36 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) = 5.778 | 5.778 | 5.778 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14810.085 0 -14810.085 -168.35964 Loop time of 4.07e-06 on 1 procs for 0 steps with 3502 atoms 172.0% 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 | | 4.07e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8094.00 ave 8094 max 8094 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: 269890.0 ave 269890 max 269890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269890 Ave neighs/atom = 77.067390 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 = 15 36 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) = 5.778 | 5.778 | 5.778 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 -14810.085 -14810.085 43.670244 107.20486 8.8423511 -168.35964 -168.35964 -307.849 -72.136921 -125.093 2.2745794 2063.0887 Loop time of 4.371e-06 on 1 procs for 0 steps with 3502 atoms 183.0% 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 | | 4.371e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8094.00 ave 8094 max 8094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134945.0 ave 134945 max 134945 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269890.0 ave 269890 max 269890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269890 Ave neighs/atom = 77.067390 Neighbor list builds = 0 Dangerous builds = 0 3502 -14810.0851123995 eV 2.27457940220675 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:47