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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -71.446822 0.0000000) to (41.247507 71.446822 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.446822 0.0000000) to (41.247507 71.446822 7.0055407) create_atoms CPU = 0.008 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.446822 0.0000000) to (41.247507 71.446822 7.0055407) create_atoms CPU = 0.008 seconds 1250 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 2488 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_478967255435_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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.251 | 5.251 | 5.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8302.0122 0 -8302.0122 3939.5802 37 0 -8337.923 0 -8337.923 950.47417 Loop time of 19.2041 on 1 procs for 37 steps with 2488 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 = -8302.01224463043 -8337.91503407551 -8337.92297354938 Force two-norm initial, final = 41.001515 0.21703210 Force max component initial, final = 4.8589769 0.031064514 Final line search alpha, max atom move = 1.0000000 0.031064514 Iterations, force evaluations = 37 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.175 | 19.175 | 19.175 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011929 | 0.011929 | 0.011929 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0174 | | | 0.09 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7240.00 ave 7240 max 7240 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: 194176.0 ave 194176 max 194176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194176 Ave neighs/atom = 78.045016 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.653 | 5.653 | 5.653 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -8337.923 0 -8337.923 950.47417 41290.703 38 0 -8337.9249 0 -8337.9249 732.03129 41302.14 Loop time of 0.917259 on 1 procs for 1 steps with 2488 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 = -8337.92297354926 -8337.92297354926 -8337.92486702911 Force two-norm initial, final = 9.2433822 5.0614778 Force max component initial, final = 8.8581065 4.8374508 Final line search alpha, max atom move = 0.00011289094 0.00054610439 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91416 | 0.91416 | 0.91416 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069958 | 0.00069958 | 0.00069958 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002401 | | | 0.26 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8161.00 ave 8161 max 8161 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: 201464.0 ave 201464 max 201464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201464 Ave neighs/atom = 80.974277 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.791 | 5.791 | 5.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8337.9249 0 -8337.9249 732.03129 Loop time of 6.205e-06 on 1 procs for 0 steps with 2488 atoms 193.4% 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 | | 6.205e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8226.00 ave 8226 max 8226 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: 201072.0 ave 201072 max 201072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201072 Ave neighs/atom = 80.816720 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.791 | 5.791 | 5.791 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 -8337.9249 -8337.9249 41.263765 142.89364 7.0047203 732.03129 732.03129 -57.175856 2440.9002 -187.63053 2.5446584 1078.3788 Loop time of 8.671e-06 on 1 procs for 0 steps with 2488 atoms 253.7% 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 | | 8.671e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8226.00 ave 8226 max 8226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100536.0 ave 100536 max 100536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201072.0 ave 201072 max 201072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201072 Ave neighs/atom = 80.816720 Neighbor list builds = 0 Dangerous builds = 0 2488 -8337.92486702911 eV 2.54465836457064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21