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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -41.306097 0.0000000) to (20.651023 41.306097 4.0499989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7656208 4.7656208 4.0499989 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.306097 0.0000000) to (20.651023 41.306097 4.0499989) create_atoms CPU = 0.002 seconds 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7656208 4.7656208 4.0499989 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.306097 0.0000000) to (20.651023 41.306097 4.0499989) create_atoms CPU = 0.001 seconds 209 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_315820974149_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1360.8297 0 -1360.8297 11805.304 42 0 -1377.9295 0 -1377.9295 97.73038 Loop time of 2.0414 on 1 procs for 42 steps with 412 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 = -1360.82974175248 -1377.92834605291 -1377.92954909894 Force two-norm initial, final = 23.878364 0.12993154 Force max component initial, final = 8.0724963 0.023057921 Final line search alpha, max atom move = 1.0000000 0.023057921 Iterations, force evaluations = 42 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0247 | 2.0247 | 2.0247 | 0.0 | 99.18 Neigh | 0.0058686 | 0.0058686 | 0.0058686 | 0.0 | 0.29 Comm | 0.0057176 | 0.0057176 | 0.0057176 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005131 | | | 0.25 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 32610.0 ave 32610 max 32610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32610 Ave neighs/atom = 79.150485 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1377.9295 0 -1377.9295 97.73038 6909.4047 45 0 -1377.9398 0 -1377.9398 710.17146 6903.826 Loop time of 0.144302 on 1 procs for 3 steps with 412 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 = -1377.92954909894 -1377.93936435548 -1377.9398194354 Force two-norm initial, final = 7.7727421 0.53500237 Force max component initial, final = 7.6756922 0.40811209 Final line search alpha, max atom move = 0.00084398998 0.00034444251 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14279 | 0.14279 | 0.14279 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036581 | 0.00036581 | 0.00036581 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001144 | | | 0.79 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 32620.0 ave 32620 max 32620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32620 Ave neighs/atom = 79.174757 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1377.9398 0 -1377.9398 710.17146 Loop time of 6.786e-06 on 1 procs for 0 steps with 412 atoms 191.6% 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 | | 6.786e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 32768.0 ave 32768 max 32768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32768 Ave neighs/atom = 79.533981 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.585 | 4.585 | 4.585 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 -1377.9398 -1377.9398 20.683203 82.612193 4.0404328 710.17146 710.17146 -73.027453 2298.029 -94.487197 2.6168369 250.52694 Loop time of 6.816e-06 on 1 procs for 0 steps with 412 atoms 264.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16384.0 ave 16384 max 16384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32768.0 ave 32768 max 32768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32768 Ave neighs/atom = 79.533981 Neighbor list builds = 0 Dangerous builds = 0 412 -1377.9398194354 eV 2.61683685890398 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02