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 -49.447903 0.0000000) to (20.187022 49.447903 6.9929895) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8448852 4.2854849 4.6619930 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -49.447903 0.0000000) to (20.187022 49.447903 6.9929895) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8448852 4.2854849 4.6619930 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.447903 0.0000000) to (20.187022 49.447903 6.9929895) create_atoms CPU = 0.001 seconds 602 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 = 6 28 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 0 atoms, new total = 1202 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 = 6 28 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4196.268 0 -4196.268 119671.33 75 0 -4804.5335 0 -4804.5335 6250.2756 Loop time of 1.18692 on 1 procs for 75 steps with 1202 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4196.26799520503 -4804.52919383592 -4804.53346949028 Force two-norm initial, final = 1732.5138 0.30839141 Force max component initial, final = 752.44421 0.074344473 Final line search alpha, max atom move = 1.0000000 0.074344473 Iterations, force evaluations = 75 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1707 | 1.1707 | 1.1707 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0083245 | 0.0083245 | 0.0083245 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007877 | | | 0.66 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6314.00 ave 6314 max 6314 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: 164148.0 ave 164148 max 164148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164148 Ave neighs/atom = 136.56240 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4804.5335 0 -4804.5335 6250.2756 13960.887 80 0 -4804.7428 0 -4804.7428 -141.66344 14011.795 Loop time of 0.0600631 on 1 procs for 5 steps with 1202 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 = -4804.53346949028 -4804.74224513655 -4804.74280581882 Force two-norm initial, final = 112.14431 2.2954507 Force max component initial, final = 103.97791 1.7041074 Final line search alpha, max atom move = 0.00023830961 0.00040610518 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057879 | 0.057879 | 0.057879 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033868 | 0.00033868 | 0.00033868 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001846 | | | 3.07 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6256.00 ave 6256 max 6256 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: 164824.0 ave 164824 max 164824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164824 Ave neighs/atom = 137.12479 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 = 6 28 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) = 5.229 | 5.229 | 5.229 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4804.7428 0 -4804.7428 -141.66344 Loop time of 3.202e-06 on 1 procs for 0 steps with 1202 atoms 124.9% 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 | | 3.202e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6246.00 ave 6246 max 6246 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: 164612.0 ave 164612 max 164612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164612 Ave neighs/atom = 136.94842 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 = 6 28 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) = 5.229 | 5.229 | 5.229 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 -4804.7428 -4804.7428 20.184272 99.313352 6.9899335 -141.66344 -141.66344 -150.36344 -79.856131 -194.77074 2.2215243 672.05314 Loop time of 2.014e-06 on 1 procs for 0 steps with 1202 atoms 248.3% 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 | | 2.014e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6246.00 ave 6246 max 6246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82306.0 ave 82306 max 82306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164612.0 ave 164612 max 164612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164612 Ave neighs/atom = 136.94842 Neighbor list builds = 0 Dangerous builds = 0 1202 -4634.7540138751 eV 2.22152434276799 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01