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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -65.496584 0.0000000) to (23.156539 65.496584 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3154199 6.9466074 5.7007459 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.496584 0.0000000) to (23.156539 65.496584 5.7007459) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3154199 6.9466074 5.7007459 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.496584 0.0000000) to (23.156539 65.496584 5.7007459) create_atoms CPU = 0.004 seconds 530 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1052 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3495.5506 0 -3495.5506 2912.5531 100 0 -3529.4108 0 -3529.4108 -1526.9643 Loop time of 2.58395 on 1 procs for 100 steps with 1052 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 = -3495.55061558439 -3529.40759339376 -3529.4107968069 Force two-norm initial, final = 25.065031 0.14015974 Force max component initial, final = 5.9769503 0.025186474 Final line search alpha, max atom move = 1.0000000 0.025186474 Iterations, force evaluations = 100 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4923 | 2.4923 | 2.4923 | 0.0 | 96.45 Neigh | 0.037123 | 0.037123 | 0.037123 | 0.0 | 1.44 Comm | 0.028729 | 0.028729 | 0.028729 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02584 | | | 1.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241.00 ave 6241 max 6241 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: 138404.0 ave 138404 max 138404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138404 Ave neighs/atom = 131.56274 Neighbor list builds = 2 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -3529.4108 0 -3529.4108 -1526.9643 17292.349 104 0 -3529.4631 0 -3529.4631 31.734427 17255.827 Loop time of 0.0829838 on 1 procs for 4 steps with 1052 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 = -3529.41079680688 -3529.46228230423 -3529.46314753254 Force two-norm initial, final = 35.776313 0.95975269 Force max component initial, final = 32.911188 0.72724612 Final line search alpha, max atom move = 0.00016556586 0.00012040713 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.079426 | 0.079426 | 0.079426 | 0.0 | 95.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078037 | 0.00078037 | 0.00078037 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002777 | | | 3.35 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6241.00 ave 6241 max 6241 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: 138944.0 ave 138944 max 138944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138944 Ave neighs/atom = 132.07605 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.166 | 5.166 | 5.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3529.4631 0 -3529.4631 31.734427 Loop time of 6.535e-06 on 1 procs for 0 steps with 1052 atoms 183.6% 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 | | 6.535e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6257.00 ave 6257 max 6257 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: 138952.0 ave 138952 max 138952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138952 Ave neighs/atom = 132.08365 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.166 | 5.166 | 5.166 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 -3529.4631 -3529.4631 23.083597 131.15681 5.699562 31.734427 31.734427 -23.608934 51.302577 67.509638 2.6724271 466.81507 Loop time of 7.096e-06 on 1 procs for 0 steps with 1052 atoms 295.9% 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 | | 7.096e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6257.00 ave 6257 max 6257 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69476.0 ave 69476 max 69476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138952.0 ave 138952 max 138952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138952 Ave neighs/atom = 132.08365 Neighbor list builds = 0 Dangerous builds = 0 1052 -3529.46314753254 eV 2.67242709172474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03