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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.487209 0.0000000) to (8.0595571 39.487209 8.8288024) create_atoms CPU = 0.000 seconds 242 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 26 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1980.9277 0 -1980.9277 -4101.3793 60 0 -1995.9143 0 -1995.9143 -20638.935 Loop time of 1.78009 on 1 procs for 60 steps with 472 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 = -1980.92767196431 -1995.91260770304 -1995.91427211116 Force two-norm initial, final = 15.436859 0.13916488 Force max component initial, final = 4.2322400 0.022577764 Final line search alpha, max atom move = 1.0000000 0.022577764 Iterations, force evaluations = 60 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.772 | 1.772 | 1.772 | 0.0 | 99.54 Neigh | 0.003098 | 0.003098 | 0.003098 | 0.0 | 0.17 Comm | 0.0025094 | 0.0025094 | 0.0025094 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002509 | | | 0.14 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2839.00 ave 2839 max 2839 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: 36648.0 ave 36648 max 36648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36648 Ave neighs/atom = 77.644068 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1995.9143 0 -1995.9143 -20638.935 5619.5225 68 0 -1996.2152 0 -1996.2152 -5808.6476 5566.0717 Loop time of 0.164214 on 1 procs for 8 steps with 472 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 = -1995.91427211117 -1996.2145837736 -1996.21516987741 Force two-norm initial, final = 82.299814 1.5104188 Force max component initial, final = 65.999502 1.4859679 Final line search alpha, max atom move = 0.00032353643 0.00048076474 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.163 | 0.163 | 0.163 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021735 | 0.00021735 | 0.00021735 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009944 | | | 0.61 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2806.00 ave 2806 max 2806 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: 36780.0 ave 36780 max 36780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36780 Ave neighs/atom = 77.923729 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1996.2152 0 -1996.2152 -5808.6476 Loop time of 1.495e-06 on 1 procs for 0 steps with 472 atoms 200.7% 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 | | 1.495e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2806.00 ave 2806 max 2806 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: 36816.0 ave 36816 max 36816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36816 Ave neighs/atom = 78.000000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.606 | 4.606 | 4.606 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 -1996.2152 -1996.2152 8.0029528 78.974418 8.8066777 -5808.6476 -5808.6476 -424.72719 -16967.693 -33.522428 2.2761261 307.57564 Loop time of 1.456e-06 on 1 procs for 0 steps with 472 atoms 137.4% 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 | | 1.456e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2806.00 ave 2806 max 2806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18408.0 ave 18408 max 18408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36816.0 ave 36816 max 36816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36816 Ave neighs/atom = 78.000000 Neighbor list builds = 0 Dangerous builds = 0 472 -1996.21516987741 eV 2.2761260602424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02