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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -66.975900 0.0000000) to (23.679557 66.975900 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0575610 6.2303163 5.1068645 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -66.975900 0.0000000) to (23.679557 66.975900 5.1068645) create_atoms CPU = 0.003 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0575610 6.2303163 5.1068645 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.975900 0.0000000) to (23.679557 66.975900 5.1068645) create_atoms CPU = 0.002 seconds 690 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 42 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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 -5743.943 0 -5743.943 23768.625 461 0 -5848.5024 0 -5848.5024 5858.1485 Loop time of 62.4654 on 1 procs for 461 steps with 1378 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 = -5743.9430122592 -5848.49740342286 -5848.50239643002 Force two-norm initial, final = 114.65286 0.23511991 Force max component initial, final = 30.358965 0.069785413 Final line search alpha, max atom move = 1.0000000 0.069785413 Iterations, force evaluations = 461 889 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.197 | 62.197 | 62.197 | 0.0 | 99.57 Neigh | 0.11679 | 0.11679 | 0.11679 | 0.0 | 0.19 Comm | 0.081739 | 0.081739 | 0.081739 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06946 | | | 0.11 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6844.00 ave 6844 max 6844 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: 123020.0 ave 123020 max 123020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123020 Ave neighs/atom = 89.274311 Neighbor list builds = 12 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 461 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.100 | 5.100 | 5.100 Mbytes Step Temp E_pair E_mol TotEng Press Volume 461 0 -5848.5024 0 -5848.5024 5858.1485 16198.562 480 0 -5851.8407 0 -5851.8407 46.791268 16244.531 Loop time of 1.65263 on 1 procs for 19 steps with 1378 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 = -5848.50239643004 -5851.84046842224 -5851.8406805597 Force two-norm initial, final = 335.84992 2.5542597 Force max component initial, final = 319.90519 1.9888103 Final line search alpha, max atom move = 0.0037713574 0.0075005146 Iterations, force evaluations = 19 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6342 | 1.6342 | 1.6342 | 0.0 | 98.88 Neigh | 0.0093483 | 0.0093483 | 0.0093483 | 0.0 | 0.57 Comm | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007581 | | | 0.46 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6915.00 ave 6915 max 6915 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: 121312.0 ave 121312 max 121312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121312 Ave neighs/atom = 88.034833 Neighbor list builds = 1 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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 -5851.8407 0 -5851.8407 46.791268 Loop time of 1.813e-06 on 1 procs for 0 steps with 1378 atoms 606.7% 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 | | 1.813e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6941.00 ave 6941 max 6941 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: 121284.0 ave 121284 max 121284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121284 Ave neighs/atom = 88.014514 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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 -5851.8407 -5851.8407 24.101645 132.97064 5.0687949 46.791268 46.791268 60.366277 -114.68395 194.69148 2.3777204 3265.3622 Loop time of 2.35e-06 on 1 procs for 0 steps with 1378 atoms 212.8% 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 | | 2.35e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6941.00 ave 6941 max 6941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60642.0 ave 60642 max 60642 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121284.0 ave 121284 max 121284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121284 Ave neighs/atom = 88.014514 Neighbor list builds = 0 Dangerous builds = 0 1378 -5851.8406805597 eV 2.37772043111609 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:04