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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4487539 6.6048871 5.7200000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4487539 6.6048871 5.7200000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.443984 0.0000000) to (21.016622 59.443984 5.7200000) create_atoms CPU = 0.001 seconds 434 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 36 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 860 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2792.2185 0 -2792.2185 15602.17 59 0 -2881.5443 0 -2881.5443 509.38369 Loop time of 3.25134 on 1 procs for 59 steps with 860 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2792.21845055063 -2881.54215012026 -2881.54425334656 Force two-norm initial, final = 174.05444 0.10739742 Force max component initial, final = 48.712307 0.0088940632 Final line search alpha, max atom move = 1.0000000 0.0088940632 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2367 | 3.2367 | 3.2367 | 0.0 | 99.55 Neigh | 0.0045357 | 0.0045357 | 0.0045357 | 0.0 | 0.14 Comm | 0.004928 | 0.004928 | 0.004928 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005193 | | | 0.16 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4194.00 ave 4194 max 4194 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: 66528.0 ave 66528 max 66528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66528 Ave neighs/atom = 77.358140 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -2881.5443 0 -2881.5443 509.38369 14292.126 62 0 -2881.564 0 -2881.564 -49.924201 14302.412 Loop time of 0.159032 on 1 procs for 3 steps with 860 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 = -2881.54425334656 -2881.56259320476 -2881.56398215585 Force two-norm initial, final = 16.370921 0.94325054 Force max component initial, final = 14.491150 0.84697213 Final line search alpha, max atom move = 0.00015522206 0.00013146876 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15794 | 0.15794 | 0.15794 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018656 | 0.00018656 | 0.00018656 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009089 | | | 0.57 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4311.00 ave 4311 max 4311 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: 66456.0 ave 66456 max 66456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66456 Ave neighs/atom = 77.274419 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.714 | 4.714 | 4.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.564 0 -2881.564 -49.924201 Loop time of 1.882e-06 on 1 procs for 0 steps with 860 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4311.00 ave 4311 max 4311 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: 66436.0 ave 66436 max 66436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66436 Ave neighs/atom = 77.251163 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.714 | 4.714 | 4.714 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 -2881.564 -2881.564 21.023408 119.11791 5.7112231 -49.924201 -49.924201 -42.999951 -12.039219 -94.733432 2.5879137 584.16428 Loop time of 2.326e-06 on 1 procs for 0 steps with 860 atoms 215.0% 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 | | 2.326e-06 | | |100.00 Nlocal: 860.000 ave 860 max 860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4311.00 ave 4311 max 4311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33218.0 ave 33218 max 33218 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66436.0 ave 66436 max 66436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66436 Ave neighs/atom = 77.251163 Neighbor list builds = 0 Dangerous builds = 0 860 -2881.56398215585 eV 2.58791366006635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03