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 -69.084383 0.0000000) to (39.885887 69.084383 6.2546062) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8848031 5.2851441 6.2546062 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.084383 0.0000000) to (39.885887 69.084383 6.2546062) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8848031 5.2851441 6.2546062 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.084383 0.0000000) to (39.885887 69.084383 6.2546062) create_atoms CPU = 0.002 seconds 1466 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 = 14 47 3 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 0 atoms, new total = 2930 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 = 14 47 3 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) = 5.780 | 5.780 | 5.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11965.289 0 -11965.289 35757.761 762 0 -12465.805 0 -12465.805 7230.2552 Loop time of 134.544 on 1 procs for 762 steps with 2930 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 = -11965.2886539538 -12465.7934192571 -12465.8049057099 Force two-norm initial, final = 489.90924 0.39962952 Force max component initial, final = 108.28420 0.094416574 Final line search alpha, max atom move = 1.0000000 0.094416574 Iterations, force evaluations = 762 1432 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 133.79 | 133.79 | 133.79 | 0.0 | 99.44 Neigh | 0.42471 | 0.42471 | 0.42471 | 0.0 | 0.32 Comm | 0.14096 | 0.14096 | 0.14096 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1911 | | | 0.14 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9113.00 ave 9113 max 9113 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: 193108.0 ave 193108 max 193108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193108 Ave neighs/atom = 65.907167 Neighbor list builds = 25 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 = 14 47 3 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 : 762 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.396 | 5.396 | 5.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 762 0 -12465.805 0 -12465.805 7230.2552 34469.034 770 0 -12467.307 0 -12467.307 -15.7959 34614.82 Loop time of 0.836116 on 1 procs for 8 steps with 2930 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 = -12465.80490571 -12467.2952560683 -12467.3070006796 Force two-norm initial, final = 408.30055 2.3756437 Force max component initial, final = 401.56702 1.8981461 Final line search alpha, max atom move = 3.9693072e-05 7.5343251e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83106 | 0.83106 | 0.83106 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065111 | 0.00065111 | 0.00065111 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004405 | | | 0.53 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9152.00 ave 9152 max 9152 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: 192784.0 ave 192784 max 192784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192784 Ave neighs/atom = 65.796587 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 = 14 47 3 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) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12467.307 0 -12467.307 -15.7959 Loop time of 1.754e-06 on 1 procs for 0 steps with 2930 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 | | 1.754e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9089.00 ave 9089 max 9089 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: 192572.0 ave 192572 max 192572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192572 Ave neighs/atom = 65.724232 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 = 14 47 3 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) = 5.534 | 5.534 | 5.534 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 -12467.307 -12467.307 39.785937 138.0465 6.3024163 -15.7959 -15.7959 53.536842 -87.779568 -13.144974 2.2595506 5418.166 Loop time of 1.777e-06 on 1 procs for 0 steps with 2930 atoms 225.1% 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 | | 1.777e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9089.00 ave 9089 max 9089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96286.0 ave 96286 max 96286 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192572.0 ave 192572 max 192572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192572 Ave neighs/atom = 65.724232 Neighbor list builds = 0 Dangerous builds = 0 2930 -12467.3070006796 eV 2.25955055801367 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:16