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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -66.588979 0.0000000) to (33.292684 66.588979 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0918222 5.0918222 3.6110986 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.588979 0.0000000) to (33.292684 66.588979 3.6110986) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0918222 5.0918222 3.6110986 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.588979 0.0000000) to (33.292684 66.588979 3.6110986) create_atoms CPU = 0.002 seconds 682 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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1358 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5689.6952 0 -5689.6952 16426.883 69 0 -5752.9471 0 -5752.9471 -73.22674 Loop time of 13.7309 on 1 procs for 69 steps with 1358 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 = -5689.69523264264 -5752.9420551297 -5752.94709033669 Force two-norm initial, final = 48.856178 0.22775985 Force max component initial, final = 13.336830 0.040986787 Final line search alpha, max atom move = 1.0000000 0.040986787 Iterations, force evaluations = 69 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.659 | 13.659 | 13.659 | 0.0 | 99.48 Neigh | 0.030868 | 0.030868 | 0.030868 | 0.0 | 0.22 Comm | 0.020222 | 0.020222 | 0.020222 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02065 | | | 0.15 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6714.00 ave 6714 max 6714 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: 105464.0 ave 105464 max 105464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105464 Ave neighs/atom = 77.661267 Neighbor list builds = 2 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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -5752.9471 0 -5752.9471 -73.22674 16011.075 76 0 -5753.1618 0 -5753.1618 -2065.9618 16029.611 Loop time of 0.9913 on 1 procs for 7 steps with 1358 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 = -5752.94709033669 -5753.16123520309 -5753.16178835732 Force two-norm initial, final = 51.760732 0.35426258 Force max component initial, final = 40.944754 0.093875857 Final line search alpha, max atom move = 0.00047979694 4.5041349e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98505 | 0.98505 | 0.98505 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012521 | 0.0012521 | 0.0012521 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005002 | | | 0.50 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6722.00 ave 6722 max 6722 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: 105448.0 ave 105448 max 105448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105448 Ave neighs/atom = 77.649485 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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5753.1618 0 -5753.1618 -2065.9618 Loop time of 6.194e-06 on 1 procs for 0 steps with 1358 atoms 193.7% 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 | | 6.194e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6730.00 ave 6730 max 6730 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: 105484.0 ave 105484 max 105484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105484 Ave neighs/atom = 77.675994 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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.190 | 5.190 | 5.190 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 -5753.1618 -5753.1618 33.122182 133.17796 3.6338893 -2065.9618 -2065.9618 9.3349378 -6211.8936 4.6731656 2.3160859 156.46943 Loop time of 6.815e-06 on 1 procs for 0 steps with 1358 atoms 278.8% 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 | | 6.815e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6730.00 ave 6730 max 6730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52742.0 ave 52742 max 52742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105484.0 ave 105484 max 105484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105484 Ave neighs/atom = 77.675994 Neighbor list builds = 0 Dangerous builds = 0 1358 -5753.16178835732 eV 2.3160858525605 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15