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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -49.119999 0.0000000) to (24.558572 49.119999 2.8548760) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9824711 3.9824711 2.8548760 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -49.119999 0.0000000) to (24.558572 49.119999 2.8548760) create_atoms CPU = 0.002 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9824711 3.9824711 2.8548760 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -49.119999 0.0000000) to (24.558572 49.119999 2.8548760) create_atoms CPU = 0.001 seconds 298 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 = 7 27 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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_634187028437_000#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 = 7 27 1 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) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2336.8498 0 -2336.8498 5427.8469 42 0 -2351.7288 0 -2351.7288 -6862.9182 Loop time of 0.844103 on 1 procs for 42 steps with 588 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 = -2336.84983961143 -2351.72660178751 -2351.72877639806 Force two-norm initial, final = 32.110525 0.13938653 Force max component initial, final = 8.8722041 0.027908539 Final line search alpha, max atom move = 1.0000000 0.027908539 Iterations, force evaluations = 42 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81345 | 0.81345 | 0.81345 | 0.0 | 96.37 Neigh | 0.011721 | 0.011721 | 0.011721 | 0.0 | 1.39 Comm | 0.011076 | 0.011076 | 0.011076 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007861 | | | 0.93 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5883.00 ave 5883 max 5883 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: 80256.0 ave 80256 max 80256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80256 Ave neighs/atom = 136.48980 Neighbor list builds = 1 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 = 7 27 1 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.526 | 4.526 | 4.526 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -2351.7288 0 -2351.7288 -6862.9182 6887.771 46 0 -2351.7796 0 -2351.7796 -1228.3706 6865.1274 Loop time of 0.063806 on 1 procs for 4 steps with 588 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2351.72877639806 -2351.77960259824 -2351.77960519602 Force two-norm initial, final = 38.585501 0.19662083 Force max component initial, final = 31.872205 0.098148962 Final line search alpha, max atom move = 0.0075128151 0.00073737501 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060826 | 0.060826 | 0.060826 | 0.0 | 95.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007162 | 0.0007162 | 0.0007162 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002264 | | | 3.55 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5883.00 ave 5883 max 5883 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: 80248.0 ave 80248 max 80248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80248 Ave neighs/atom = 136.47619 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 = 7 27 1 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) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2351.7796 0 -2351.7796 -1228.3706 Loop time of 6.164e-06 on 1 procs for 0 steps with 588 atoms 178.5% 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 | | 6.164e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5885.00 ave 5885 max 5885 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: 80292.0 ave 80292 max 80292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80292 Ave neighs/atom = 136.55102 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 = 7 27 1 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) = 4.664 | 4.664 | 4.664 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 -2351.7796 -2351.7796 24.551764 98.239997 2.8462796 -1228.3706 -1228.3706 22.899556 -3726.8995 18.888215 2.2565104 219.17852 Loop time of 6.265e-06 on 1 procs for 0 steps with 588 atoms 303.3% 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 | | 6.265e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5885.00 ave 5885 max 5885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40146.0 ave 40146 max 40146 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80292.0 ave 80292 max 80292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80292 Ave neighs/atom = 136.55102 Neighbor list builds = 0 Dangerous builds = 0 588 -2268.62369033503 eV 2.25651040818774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01