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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -32.088731 0.0000000) to (16.044366 32.088731 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7025459 3.7025459 3.1465590 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -32.088731 0.0000000) to (16.044366 32.088731 3.1465590) create_atoms CPU = 0.002 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7025459 3.7025459 3.1465590 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -32.088731 0.0000000) to (16.044366 32.088731 3.1465590) create_atoms CPU = 0.001 seconds 106 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 20 1 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 208 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_356501945107_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1313.9502 0 -1313.9502 148361.99 36 0 -1406.3685 0 -1406.3685 12814.742 Loop time of 1.1918 on 1 procs for 36 steps with 208 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 = -1313.95021042423 -1406.36752847786 -1406.36853436748 Force two-norm initial, final = 240.93143 0.17657946 Force max component initial, final = 84.696320 0.033905160 Final line search alpha, max atom move = 1.0000000 0.033905160 Iterations, force evaluations = 36 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1846 | 1.1846 | 1.1846 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039065 | 0.0039065 | 0.0039065 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003262 | | | 0.27 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2052.00 ave 2052 max 2052 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: 13508.0 ave 13508 max 13508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13508 Ave neighs/atom = 64.942308 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1406.3685 0 -1406.3685 12814.742 3239.9698 46 0 -1406.6449 0 -1406.6449 234.34317 3255.3516 Loop time of 0.209626 on 1 procs for 10 steps with 208 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 = -1406.36853436748 -1406.6444283986 -1406.64494905243 Force two-norm initial, final = 66.137958 2.3028277 Force max component initial, final = 65.223078 1.9359562 Final line search alpha, max atom move = 0.0046343521 0.0089719028 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20682 | 0.20682 | 0.20682 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063695 | 0.00063695 | 0.00063695 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002164 | | | 1.03 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2052.00 ave 2052 max 2052 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: 13316.0 ave 13316 max 13316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13316 Ave neighs/atom = 64.019231 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1406.6449 0 -1406.6449 234.34317 Loop time of 2.9628e-05 on 1 procs for 0 steps with 208 atoms 40.5% 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 | | 2.963e-05 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2052.00 ave 2052 max 2052 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: 13308.0 ave 13308 max 13308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13308 Ave neighs/atom = 63.980769 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.534 | 4.534 | 4.534 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 -1406.6449 -1406.6449 16.01599 64.742956 3.1394357 234.34317 234.34317 951.12856 206.40368 -454.50273 2.5052932 147.813 Loop time of 7.257e-06 on 1 procs for 0 steps with 208 atoms 261.8% 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 | | 7.257e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2052.00 ave 2052 max 2052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6654.00 ave 6654 max 6654 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13308.0 ave 13308 max 13308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13308 Ave neighs/atom = 63.980769 Neighbor list builds = 0 Dangerous builds = 0 208 -1406.64494905243 eV 2.50529318068833 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01