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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -51.322164 0.0000000) to (12.096750 51.322164 5.1580716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4985228 6.2208684 5.1580716 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -51.322164 0.0000000) to (12.096750 51.322164 5.1580716) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4985228 6.2208684 5.1580716 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.322164 0.0000000) to (12.096750 51.322164 5.1580716) create_atoms CPU = 0.001 seconds 266 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 39 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 530 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.874 | 4.874 | 4.874 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2060.3451 0 -2060.3451 61483.684 36 0 -2191.8276 0 -2191.8276 10837.288 Loop time of 1.76628 on 1 procs for 36 steps with 530 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 = -2060.34506988496 -2191.82602545342 -2191.82762388809 Force two-norm initial, final = 418.11690 0.15557994 Force max component initial, final = 149.95429 0.032523967 Final line search alpha, max atom move = 1.0000000 0.032523967 Iterations, force evaluations = 36 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.762 | 1.762 | 1.762 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019546 | 0.0019546 | 0.0019546 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002355 | | | 0.13 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2812.00 ave 2812 max 2812 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: 28704.0 ave 28704 max 28704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28704 Ave neighs/atom = 54.158491 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.874 | 4.874 | 4.874 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -2191.8276 0 -2191.8276 10837.288 6404.5856 45 0 -2192.1549 0 -2192.1549 -120.43625 6446.1962 Loop time of 0.332741 on 1 procs for 9 steps with 530 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 = -2191.82762388809 -2192.15475355743 -2192.15486016017 Force two-norm initial, final = 93.225433 1.0443256 Force max component initial, final = 88.157869 0.74981391 Final line search alpha, max atom move = 0.00083850637 0.00062872374 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33094 | 0.33094 | 0.33094 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026833 | 0.00026833 | 0.00026833 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001529 | | | 0.46 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2812.00 ave 2812 max 2812 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: 28540.0 ave 28540 max 28540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28540 Ave neighs/atom = 53.849057 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.012 | 5.012 | 5.012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2192.1549 0 -2192.1549 -120.43625 Loop time of 1.916e-06 on 1 procs for 0 steps with 530 atoms 156.6% 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 | | 1.916e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2812.00 ave 2812 max 2812 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: 28504.0 ave 28504 max 28504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28504 Ave neighs/atom = 53.781132 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.012 | 5.012 | 5.012 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 -2192.1549 -2192.1549 12.090373 103.44715 5.1540103 -120.43625 -120.43625 -186.26502 -146.75256 -28.291158 2.3393716 203.52091 Loop time of 2.378e-06 on 1 procs for 0 steps with 530 atoms 210.3% 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 | | 2.378e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2812.00 ave 2812 max 2812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14252.0 ave 14252 max 14252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28504.0 ave 28504 max 28504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28504 Ave neighs/atom = 53.781132 Neighbor list builds = 0 Dangerous builds = 0 530 -2192.15486016017 eV 2.33937163324864 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02