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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -55.406947 0.0000000) to (33.927533 55.406947 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4721827 5.3616221 5.7450679 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.406947 0.0000000) to (33.927533 55.406947 8.6176019) create_atoms CPU = 0.002 seconds 1493 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4721827 5.3616221 5.7450679 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.406947 0.0000000) to (33.927533 55.406947 8.6176019) create_atoms CPU = 0.002 seconds 1493 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 26 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2952 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_222110751402_000#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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.871 | 7.871 | 7.871 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12838.398 0 -12838.398 10900.13 56 0 -12907.087 0 -12907.087 -6953.3762 Loop time of 3.83159 on 1 procs for 56 steps with 2952 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 = -12838.3975964328 -12907.076847986 -12907.0872316765 Force two-norm initial, final = 118.67207 0.31710087 Force max component initial, final = 16.516908 0.060798568 Final line search alpha, max atom move = 1.0000000 0.060798568 Iterations, force evaluations = 56 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7652 | 3.7652 | 3.7652 | 0.0 | 98.27 Neigh | 0.041622 | 0.041622 | 0.041622 | 0.0 | 1.09 Comm | 0.012176 | 0.012176 | 0.012176 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01263 | | | 0.33 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13018.0 ave 13018 max 13018 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: 725750.0 ave 725750 max 725750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 725750 Ave neighs/atom = 245.85027 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.871 | 7.871 | 7.871 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -12907.087 0 -12907.087 -6953.3762 32399.098 59 0 -12907.273 0 -12907.273 -1782.3888 32303.284 Loop time of 0.227307 on 1 procs for 3 steps with 2952 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 = -12907.0872316764 -12907.2721104579 -12907.2725041822 Force two-norm initial, final = 174.22644 0.35167004 Force max component initial, final = 134.14414 0.069514870 Final line search alpha, max atom move = 0.00022320059 1.5515760e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22412 | 0.22412 | 0.22412 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053512 | 0.00053512 | 0.00053512 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002651 | | | 1.17 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12916.0 ave 12916 max 12916 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: 727114.0 ave 727114 max 727114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 727114 Ave neighs/atom = 246.31233 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 8.009 | 8.009 | 8.009 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12907.273 0 -12907.273 -1782.3888 Loop time of 2.08e-06 on 1 procs for 0 steps with 2952 atoms 144.2% 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 | | 2.08e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12941.0 ave 12941 max 12941 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: 727398.0 ave 727398 max 727398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 727398 Ave neighs/atom = 246.40854 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 8.009 | 8.009 | 8.009 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 -12907.273 -12907.273 33.867822 110.81389 8.6072653 -1782.3888 -1782.3888 -2.1239405 -5341.5987 -3.4436592 2.1923107 868.51394 Loop time of 2.45e-06 on 1 procs for 0 steps with 2952 atoms 244.9% 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 | | 2.45e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12941.0 ave 12941 max 12941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 363699.0 ave 363699 max 363699 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 727398.0 ave 727398 max 727398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 727398 Ave neighs/atom = 246.40854 Neighbor list builds = 0 Dangerous builds = 0 2952 -12907.2725041822 eV 2.19231067284826 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04