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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -45.687928 0.0000000) to (16.151737 45.687928 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6507152 6.7182369 5.5400000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -45.687928 0.0000000) to (16.151737 45.687928 5.5400000) create_atoms CPU = 0.003 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6507152 6.7182369 5.5400000 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -45.687928 0.0000000) to (16.151737 45.687928 5.5400000) create_atoms CPU = 0.002 seconds 274 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 29 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 542 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_070797404269_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3085.3009 0 -3085.3009 15636.998 19 0 -3114.6216 0 -3114.6216 3159.1993 Loop time of 0.701211 on 1 procs for 19 steps with 542 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 = -3085.300893012 -3114.61892549808 -3114.6216059704 Force two-norm initial, final = 43.377127 0.19620744 Force max component initial, final = 11.502854 0.048362627 Final line search alpha, max atom move = 1.0000000 0.048362627 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69548 | 0.69548 | 0.69548 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028037 | 0.0028037 | 0.0028037 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002928 | | | 0.42 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3336.00 ave 3336 max 3336 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: 41992.0 ave 41992 max 41992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41992 Ave neighs/atom = 77.476015 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -3114.6216 0 -3114.6216 3159.1993 8176.3685 20 0 -3114.6239 0 -3114.6239 1987.3482 8181.676 Loop time of 0.0609224 on 1 procs for 1 steps with 542 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 = -3114.6216059704 -3114.6216059704 -3114.62391174233 Force two-norm initial, final = 10.038626 0.44770175 Force max component initial, final = 7.7650747 0.33424692 Final line search alpha, max atom move = 0.00012878176 4.3044907e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06001 | 0.06001 | 0.06001 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021002 | 0.00021002 | 0.00021002 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007028 | | | 1.15 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3336.00 ave 3336 max 3336 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: 41844.0 ave 41844 max 41844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41844 Ave neighs/atom = 77.202952 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3114.6239 0 -3114.6239 1987.3482 Loop time of 6.355e-06 on 1 procs for 0 steps with 542 atoms 173.1% 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 | | 6.355e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3336.00 ave 3336 max 3336 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: 41844.0 ave 41844 max 41844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41844 Ave neighs/atom = 77.202952 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.634 | 4.634 | 4.634 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 -3114.6239 -3114.6239 16.1575 91.375856 5.5416189 1987.3482 1987.3482 43.837496 5983.6802 -65.473021 2.5770957 381.18447 Loop time of 6.435e-06 on 1 procs for 0 steps with 542 atoms 264.2% 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 | | 6.435e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3336.00 ave 3336 max 3336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20922.0 ave 20922 max 20922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41844.0 ave 41844 max 41844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41844 Ave neighs/atom = 77.202952 Neighbor list builds = 0 Dangerous builds = 0 542 -3114.62391174233 eV 2.57709565143515 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01