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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -34.566525 0.0000000) to (28.223449 34.566525 6.9834925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0319213 3.9974892 4.6556617 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.566525 0.0000000) to (28.223449 34.566525 6.9834925) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0319213 3.9974892 4.6556617 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.566525 0.0000000) to (28.223449 34.566525 6.9834925) create_atoms CPU = 0.001 seconds 590 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 20 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1172 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2581.3999 0 -2581.3999 354287.77 109 0 -4989.3046 0 -4989.3046 5099.5407 Loop time of 12.0095 on 1 procs for 109 steps with 1172 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2581.39993270017 -4989.29985600494 -4989.30462342535 Force two-norm initial, final = 3803.2056 0.29911279 Force max component initial, final = 943.43397 0.063063913 Final line search alpha, max atom move = 1.0000000 0.063063913 Iterations, force evaluations = 109 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.932 | 11.932 | 11.932 | 0.0 | 99.35 Neigh | 0.047653 | 0.047653 | 0.047653 | 0.0 | 0.40 Comm | 0.01399 | 0.01399 | 0.01399 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.016 | | | 0.13 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5191.00 ave 5191 max 5191 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: 152816.0 ave 152816 max 152816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152816 Ave neighs/atom = 130.38908 Neighbor list builds = 5 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -4989.3046 0 -4989.3046 5099.5407 13626.003 120 0 -4990.1511 0 -4990.1511 55.012415 13663.327 Loop time of 0.874293 on 1 procs for 11 steps with 1172 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 = -4989.30462342535 -4990.15099400782 -4990.15109079499 Force two-norm initial, final = 166.01613 1.5964472 Force max component initial, final = 163.75225 1.0145275 Final line search alpha, max atom move = 0.0019666554 0.0019952260 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8695 | 0.8695 | 0.8695 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069292 | 0.00069292 | 0.00069292 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004099 | | | 0.47 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5222.00 ave 5222 max 5222 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: 153152.0 ave 153152 max 153152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153152 Ave neighs/atom = 130.67577 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.178 | 5.178 | 5.178 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4990.1511 0 -4990.1511 55.012415 Loop time of 2.074e-06 on 1 procs for 0 steps with 1172 atoms 144.6% 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 | | 2.074e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5273.00 ave 5273 max 5273 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: 151908.0 ave 151908 max 151908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151908 Ave neighs/atom = 129.61433 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.178 | 5.178 | 5.178 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 -4990.1511 -4990.1511 28.106167 69.809476 6.9637063 55.012415 55.012415 118.47024 85.499392 -38.932386 2.2920527 1076.3619 Loop time of 2.058e-06 on 1 procs for 0 steps with 1172 atoms 291.5% 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 | | 2.058e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5273.00 ave 5273 max 5273 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75954.0 ave 75954 max 75954 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151908.0 ave 151908 max 151908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151908 Ave neighs/atom = 129.61433 Neighbor list builds = 0 Dangerous builds = 0 1172 -4990.15109079499 eV 2.29205267818272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13