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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -42.254770 0.0000000) to (34.500876 42.254770 6.9940594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2535326 4.0518273 4.6627062 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -42.254770 0.0000000) to (34.500876 42.254770 6.9940594) create_atoms CPU = 0.001 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2535326 4.0518273 4.6627062 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.254770 0.0000000) to (34.500876 42.254770 6.9940594) create_atoms CPU = 0.001 seconds 877 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1744 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_884343146310_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5117.3289 0 -5117.3289 216531.38 112 0 -6959.9113 0 -6959.9113 1538.5205 Loop time of 2.47218 on 1 procs for 112 steps with 1744 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5117.3289017598 -6959.90560744427 -6959.91133616331 Force two-norm initial, final = 3438.2749 0.26414587 Force max component initial, final = 753.26824 0.017155311 Final line search alpha, max atom move = 1.0000000 0.017155311 Iterations, force evaluations = 112 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3964 | 2.3964 | 2.3964 | 0.0 | 96.93 Neigh | 0.046461 | 0.046461 | 0.046461 | 0.0 | 1.88 Comm | 0.012984 | 0.012984 | 0.012984 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01635 | | | 0.66 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6956.00 ave 6956 max 6956 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: 237830.0 ave 237830 max 237830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237830 Ave neighs/atom = 136.37041 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -6959.9113 0 -6959.9113 1538.5205 20392.251 117 0 -6960.1157 0 -6960.1157 62.35731 20410.202 Loop time of 0.0992506 on 1 procs for 5 steps with 1744 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 = -6959.91133616328 -6960.11556964542 -6960.11569940115 Force two-norm initial, final = 98.707924 1.5295427 Force max component initial, final = 92.949951 1.1985232 Final line search alpha, max atom move = 0.00040476578 0.00048512120 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096213 | 0.096213 | 0.096213 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042167 | 0.00042167 | 0.00042167 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002616 | | | 2.64 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237336.0 ave 237336 max 237336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237336 Ave neighs/atom = 136.08716 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6960.1157 0 -6960.1157 62.35731 Loop time of 1.899e-06 on 1 procs for 0 steps with 1744 atoms 158.0% 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 | | 1.899e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237168.0 ave 237168 max 237168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237168 Ave neighs/atom = 135.99083 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 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 -6960.1157 -6960.1157 34.463999 84.826306 6.9815375 62.35731 62.35731 36.138628 57.019099 93.914204 2.2462534 1132.3987 Loop time of 2.089e-06 on 1 procs for 0 steps with 1744 atoms 191.5% 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 | | 2.089e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118584.0 ave 118584 max 118584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237168.0 ave 237168 max 237168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237168 Ave neighs/atom = 135.99083 Neighbor list builds = 0 Dangerous builds = 0 1744 -6960.11569940115 eV 2.24625336991371 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03