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 -65.399776 0.0000000) to (23.122313 65.399776 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2035473 5.5829077 5.1068645 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.399776 0.0000000) to (23.122313 65.399776 5.1068645) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2035473 5.5829077 5.1068645 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.399776 0.0000000) to (23.122313 65.399776 5.1068645) create_atoms CPU = 0.002 seconds 658 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 41 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 8 atoms, new total = 1306 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 41 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5409.1671 0 -5409.1671 17784.017 600 0 -5547.5546 0 -5547.5546 -3256.699 Loop time of 89.2969 on 1 procs for 600 steps with 1306 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 = -5409.16713315571 -5547.54920200761 -5547.55460318402 Force two-norm initial, final = 231.52011 0.23646583 Force max component initial, final = 76.143019 0.049265239 Final line search alpha, max atom move = 0.92969118 0.045801459 Iterations, force evaluations = 600 1137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 88.947 | 88.947 | 88.947 | 0.0 | 99.61 Neigh | 0.16083 | 0.16083 | 0.16083 | 0.0 | 0.18 Comm | 0.10147 | 0.10147 | 0.10147 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08794 | | | 0.10 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6520.00 ave 6520 max 6520 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: 117912.0 ave 117912 max 117912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117912 Ave neighs/atom = 90.284839 Neighbor list builds = 17 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 41 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 : 600 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press Volume 600 0 -5547.5546 0 -5547.5546 -3256.699 15445.14 622 0 -5553.2602 0 -5553.2602 31.404385 15406.054 Loop time of 2.32891 on 1 procs for 22 steps with 1306 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 = -5547.554603184 -5553.25934357066 -5553.2601816768 Force two-norm initial, final = 413.69205 5.2569528 Force max component initial, final = 288.17353 3.9764236 Final line search alpha, max atom move = 0.0017578674 0.0069900255 Iterations, force evaluations = 22 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3 | 2.3 | 2.3 | 0.0 | 98.76 Neigh | 0.018735 | 0.018735 | 0.018735 | 0.0 | 0.80 Comm | 0.0018151 | 0.0018151 | 0.0018151 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008402 | | | 0.36 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6664.00 ave 6664 max 6664 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: 120080.0 ave 120080 max 120080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120080 Ave neighs/atom = 91.944870 Neighbor list builds = 2 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5553.2602 0 -5553.2602 31.404385 Loop time of 2.283e-06 on 1 procs for 0 steps with 1306 atoms 175.2% 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 | | 2.283e-06 | | |100.00 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6679.00 ave 6679 max 6679 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: 120242.0 ave 120242 max 120242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120242 Ave neighs/atom = 92.068913 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) = 5.216 | 5.216 | 5.216 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 -5553.2602 -5553.2602 22.968412 133.53151 5.0231564 31.404385 31.404385 410.78189 -22.56448 -294.00426 2.3716426 3477.0584 Loop time of 2.625e-06 on 1 procs for 0 steps with 1306 atoms 190.5% 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 | | 2.625e-06 | | |100.00 Nlocal: 1306.00 ave 1306 max 1306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6679.00 ave 6679 max 6679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60121.0 ave 60121 max 60121 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120242.0 ave 120242 max 120242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120242 Ave neighs/atom = 92.068913 Neighbor list builds = 0 Dangerous builds = 0 1306 -5553.26018167679 eV 2.37164262482336 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:32