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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -53.054301 0.0000000) to (18.756517 53.054301 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7981787 4.9350178 4.0451344 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.054301 0.0000000) to (18.756517 53.054301 4.0451344) create_atoms CPU = 0.001 seconds 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7981787 4.9350178 4.0451344 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.054301 0.0000000) to (18.756517 53.054301 4.0451344) create_atoms CPU = 0.001 seconds 346 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 688 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.952 | 4.952 | 4.952 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2906.2758 0 -2906.2758 20527.704 142 0 -3016.5147 0 -3016.5147 1532.4333 Loop time of 1.47752 on 1 procs for 142 steps with 688 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 = -2906.27576485519 -3016.51234124002 -3016.51471908349 Force two-norm initial, final = 85.131000 0.18080957 Force max component initial, final = 21.433665 0.015641799 Final line search alpha, max atom move = 1.0000000 0.015641799 Iterations, force evaluations = 142 262 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4354 | 1.4354 | 1.4354 | 0.0 | 97.15 Neigh | 0.020724 | 0.020724 | 0.020724 | 0.0 | 1.40 Comm | 0.01282 | 0.01282 | 0.01282 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008603 | | | 0.58 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6647.00 ave 6647 max 6647 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: 111500.0 ave 111500 max 111500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111500 Ave neighs/atom = 162.06395 Neighbor list builds = 3 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 142 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -3016.5147 0 -3016.5147 1532.4333 8050.739 172 0 -3019.9571 0 -3019.9571 19391.206 7919.3945 Loop time of 0.18484 on 1 procs for 30 steps with 688 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 = -3016.5147190835 -3019.95477006329 -3019.95708522181 Force two-norm initial, final = 239.52603 4.7003270 Force max component initial, final = 234.72037 3.8658085 Final line search alpha, max atom move = 0.00017439463 0.00067417623 Iterations, force evaluations = 30 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17668 | 0.17668 | 0.17668 | 0.0 | 95.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014889 | 0.0014889 | 0.0014889 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006668 | | | 3.61 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6532.00 ave 6532 max 6532 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: 111168.0 ave 111168 max 111168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111168 Ave neighs/atom = 161.58140 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3019.9571 0 -3019.9571 19391.206 Loop time of 1.758e-06 on 1 procs for 0 steps with 688 atoms 170.6% 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 | | 1.758e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 113888.0 ave 113888 max 113888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113888 Ave neighs/atom = 165.53488 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.092 | 5.092 | 5.092 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 -3019.9571 -3019.9571 18.209982 106.1086 4.0985653 19391.206 19391.206 454.0714 56927.123 792.424 2.4659844 3821.562 Loop time of 1.494e-06 on 1 procs for 0 steps with 688 atoms 133.9% 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 | | 1.494e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56944.0 ave 56944 max 56944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113888.0 ave 113888 max 113888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113888 Ave neighs/atom = 165.53488 Neighbor list builds = 0 Dangerous builds = 0 688 -3019.95708522181 eV 2.46598438291706 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01