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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -51.863040 0.0000000) to (18.336354 51.863040 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9195095 4.4273327 4.0498230 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -51.863040 0.0000000) to (18.336354 51.863040 4.0498230) create_atoms CPU = 0.004 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9195095 4.4273327 4.0498230 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -51.863040 0.0000000) to (18.336354 51.863040 4.0498230) create_atoms CPU = 0.003 seconds 330 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 ghost atom cutoff = 6 binsize = 3, bins = 7 35 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 656 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_321233176498_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 ghost atom cutoff = 6 binsize = 3, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2596.4504 0 -2596.4504 58545.315 94 0 -2804.542 0 -2804.542 5938.1967 Loop time of 7.83953 on 1 procs for 94 steps with 656 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2596.45044150079 -2804.53993257058 -2804.54199129947 Force two-norm initial, final = 450.40986 0.13586235 Force max component initial, final = 145.96039 0.029197335 Final line search alpha, max atom move = 1.0000000 0.029197335 Iterations, force evaluations = 94 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7928 | 7.7928 | 7.7928 | 0.0 | 99.40 Neigh | 0.014545 | 0.014545 | 0.014545 | 0.0 | 0.19 Comm | 0.016272 | 0.016272 | 0.016272 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01593 | | | 0.20 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3571.00 ave 3571 max 3571 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: 42168.0 ave 42168 max 42168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42168 Ave neighs/atom = 64.280488 Neighbor list builds = 2 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 ghost atom cutoff = 6 binsize = 3, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -2804.542 0 -2804.542 5938.1967 7702.5936 101 0 -2804.7529 0 -2804.7529 -114.6676 7729.418 Loop time of 0.3968 on 1 procs for 7 steps with 656 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 = -2804.54199129947 -2804.75271819616 -2804.75294035717 Force two-norm initial, final = 72.539189 1.0275884 Force max component initial, final = 71.850652 0.68210720 Final line search alpha, max atom move = 0.00054985101 0.00037505733 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39328 | 0.39328 | 0.39328 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074463 | 0.00074463 | 0.00074463 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00277 | | | 0.70 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3583.00 ave 3583 max 3583 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: 42128.0 ave 42128 max 42128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42128 Ave neighs/atom = 64.219512 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 ghost atom cutoff = 6 binsize = 3, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.652 | 4.652 | 4.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2804.7529 0 -2804.7529 -114.6676 Loop time of 6.616e-06 on 1 procs for 0 steps with 656 atoms 196.5% 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 | | 6.616e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3583.00 ave 3583 max 3583 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: 42092.0 ave 42092 max 42092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42092 Ave neighs/atom = 64.164634 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 ghost atom cutoff = 6 binsize = 3, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.652 | 4.652 | 4.652 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 -2804.7529 -2804.7529 18.314864 104.36808 4.043667 -114.6676 -114.6676 -137.4507 -65.37784 -141.17426 2.2776055 313.34352 Loop time of 6.775e-06 on 1 procs for 0 steps with 656 atoms 295.2% 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 | | 6.775e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3583.00 ave 3583 max 3583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21046.0 ave 21046 max 21046 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42092.0 ave 42092 max 42092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42092 Ave neighs/atom = 64.164634 Neighbor list builds = 0 Dangerous builds = 0 656 -2804.75294035717 eV 2.27760548029809 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08