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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -40.376920 0.0000000) to (8.0746618 40.376920 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8447971 4.8447971 3.6110985 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -40.376920 0.0000000) to (8.0746618 40.376920 3.6110985) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8447971 4.8447971 3.6110985 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -40.376920 0.0000000) to (8.0746618 40.376920 3.6110985) create_atoms CPU = 0.001 seconds 102 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 3 24 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 200 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.418 | 4.418 | 4.418 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -833.81298 0 -833.81298 25485.881 15 0 -844.47512 0 -844.47512 8851.8181 Loop time of 0.891684 on 1 procs for 15 steps with 200 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 = -833.812976778605 -844.474431125457 -844.475115321648 Force two-norm initial, final = 31.566456 0.074418456 Force max component initial, final = 11.196936 0.016572579 Final line search alpha, max atom move = 1.0000000 0.016572579 Iterations, force evaluations = 15 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88831 | 0.88831 | 0.88831 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018556 | 0.0018556 | 0.0018556 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001515 | | | 0.17 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 26368.0 ave 26368 max 26368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26368 Ave neighs/atom = 131.84000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.418 | 4.418 | 4.418 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -844.47512 0 -844.47512 8851.8181 2354.6527 25 0 -844.557 0 -844.557 -1631.7707 2369.0064 Loop time of 0.395943 on 1 procs for 10 steps with 200 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 = -844.475115321648 -844.556294478235 -844.557002865618 Force two-norm initial, final = 22.168866 0.48704498 Force max component initial, final = 20.117169 0.30080794 Final line search alpha, max atom move = 0.0011275106 0.00033916413 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39255 | 0.39255 | 0.39255 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076417 | 0.00076417 | 0.00076417 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002625 | | | 0.66 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 26088.0 ave 26088 max 26088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26088 Ave neighs/atom = 130.44000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.555 | 4.555 | 4.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -844.557 0 -844.557 -1631.7707 Loop time of 7.017e-06 on 1 procs for 0 steps with 200 atoms 171.0% 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 | | 7.017e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 25904.0 ave 25904 max 25904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25904 Ave neighs/atom = 129.52000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.555 | 4.555 | 4.555 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 -844.557 -844.557 8.0436119 80.75384 3.6471358 -1631.7707 -1631.7707 -202.65634 -4495.072 -197.58373 2.3401264 107.21097 Loop time of 6.304e-06 on 1 procs for 0 steps with 200 atoms 237.9% 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 | | 6.304e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12952.0 ave 12952 max 12952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25904.0 ave 25904 max 25904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25904 Ave neighs/atom = 129.52000 Neighbor list builds = 0 Dangerous builds = 0 200 -844.557002865618 eV 2.34012643275157 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01