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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) create_atoms CPU = 0.004 seconds 1610 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_101214310689_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 12.15 | 12.15 | 12.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14170.088 0 -14170.088 3614.5325 97 0 -14268.204 0 -14268.204 6161.6207 Loop time of 8.64576 on 1 procs for 97 steps with 3216 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 = -14170.0884535351 -14268.1913160992 -14268.2043416017 Force two-norm initial, final = 37.174293 0.36974901 Force max component initial, final = 5.1925149 0.045189557 Final line search alpha, max atom move = 1.0000000 0.045189557 Iterations, force evaluations = 97 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4233 | 8.4233 | 8.4233 | 0.0 | 97.43 Neigh | 0.14101 | 0.14101 | 0.14101 | 0.0 | 1.63 Comm | 0.044893 | 0.044893 | 0.044893 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03657 | | | 0.42 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17388.0 ave 17388 max 17388 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: 795200.0 ave 795200 max 795200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795200 Ave neighs/atom = 247.26368 Neighbor list builds = 3 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.16 | 12.16 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -14268.204 0 -14268.204 6161.6207 35065.824 102 0 -14268.776 0 -14268.776 32.428723 35186.137 Loop time of 0.354555 on 1 procs for 5 steps with 3216 atoms 95.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14268.2043416018 -14268.7749029477 -14268.7764604488 Force two-norm initial, final = 296.36044 1.3335557 Force max component initial, final = 277.11710 0.76837419 Final line search alpha, max atom move = 0.00011778173 9.0500443e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34729 | 0.34729 | 0.34729 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001266 | 0.001266 | 0.001266 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006001 | | | 1.69 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17396.0 ave 17396 max 17396 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: 795648.0 ave 795648 max 795648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795648 Ave neighs/atom = 247.40299 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 11.67 | 11.67 | 11.67 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14268.776 0 -14268.776 32.428723 Loop time of 2.852e-06 on 1 procs for 0 steps with 3216 atoms 175.3% 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 | | 2.852e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17372.0 ave 17372 max 17372 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: 795092.0 ave 795092 max 795092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795092 Ave neighs/atom = 247.23010 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 11.67 | 11.67 | 11.67 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 -14268.776 -14268.776 40.751053 141.74187 6.0916451 32.428723 32.428723 31.466977 35.13371 30.685483 2.2038571 997.39764 Loop time of 2.833e-06 on 1 procs for 0 steps with 3216 atoms 247.1% 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 | | 2.833e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17372.0 ave 17372 max 17372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397546.0 ave 397546 max 397546 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 795092.0 ave 795092 max 795092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795092 Ave neighs/atom = 247.23010 Neighbor list builds = 0 Dangerous builds = 0 3216 -14196.2567855532 eV 2.20385711257988 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09