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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -57.806762 0.0000000) to (40.872692 57.806762 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4114027 5.1002396 5.7233217 Created 820 atoms using lattice units in orthogonal box = (0.0000000 -57.806762 0.0000000) to (40.872692 57.806762 5.7233217) create_atoms CPU = 0.001 seconds 820 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4114027 5.1002396 5.7233217 Created 820 atoms using lattice units in orthogonal box = (0.0000000 -57.806762 0.0000000) to (40.872692 57.806762 5.7233217) create_atoms CPU = 0.001 seconds 820 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 33 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1626 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5384.9037 0 -5384.9037 9993.5086 49 0 -5448.2135 0 -5448.2135 -235.37729 Loop time of 6.49462 on 1 procs for 49 steps with 1626 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 = -5384.90366148855 -5448.20865403563 -5448.21349691554 Force two-norm initial, final = 41.514883 0.20329118 Force max component initial, final = 5.4617471 0.040324018 Final line search alpha, max atom move = 1.0000000 0.040324018 Iterations, force evaluations = 49 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4674 | 6.4674 | 6.4674 | 0.0 | 99.58 Neigh | 0.010462 | 0.010462 | 0.010462 | 0.0 | 0.16 Comm | 0.0078858 | 0.0078858 | 0.0078858 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008867 | | | 0.14 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368.00 ave 6368 max 6368 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: 139080.0 ave 139080 max 139080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139080 Ave neighs/atom = 85.535055 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -5448.2135 0 -5448.2135 -235.37729 27045.19 50 0 -5448.2177 0 -5448.2177 350.93743 27024.958 Loop time of 0.239366 on 1 procs for 1 steps with 1626 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 = -5448.21349691554 -5448.21349691554 -5448.21770516962 Force two-norm initial, final = 15.845447 0.51917370 Force max component initial, final = 11.706093 0.34544770 Final line search alpha, max atom move = 8.5425601e-05 2.9510077e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23842 | 0.23842 | 0.23842 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015991 | 0.00015991 | 0.00015991 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007895 | | | 0.33 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6369.00 ave 6369 max 6369 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: 139132.0 ave 139132 max 139132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139132 Ave neighs/atom = 85.567036 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.257 | 5.257 | 5.257 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5448.2177 0 -5448.2177 350.93743 Loop time of 2.173e-06 on 1 procs for 0 steps with 1626 atoms 184.1% 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 | | 2.173e-06 | | |100.00 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6369.00 ave 6369 max 6369 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: 139144.0 ave 139144 max 139144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139144 Ave neighs/atom = 85.574416 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.257 | 5.257 | 5.257 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 -5448.2177 -5448.2177 40.858103 115.61352 5.721082 350.93743 350.93743 19.515848 1053.7683 -20.471877 2.5767861 1012.9644 Loop time of 2.078e-06 on 1 procs for 0 steps with 1626 atoms 192.5% 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 | | 2.078e-06 | | |100.00 Nlocal: 1626.00 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6369.00 ave 6369 max 6369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69572.0 ave 69572 max 69572 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139144.0 ave 139144 max 139144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139144 Ave neighs/atom = 85.574416 Neighbor list builds = 0 Dangerous builds = 0 1626 -5448.21770516962 eV 2.57678606637775 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07