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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -56.095903 0.0000000) to (19.832897 56.095903 4.8825217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4089719 5.9495655 4.8825217 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -56.095903 0.0000000) to (19.832897 56.095903 4.8825217) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4089719 5.9495655 4.8825217 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -56.095903 0.0000000) to (19.832897 56.095903 4.8825217) create_atoms CPU = 0.005 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 5 29 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.454 | 5.454 | 5.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4617.1383 0 -4617.1383 48966.49 58 0 -4752.0602 0 -4752.0602 23334.697 Loop time of 2.66398 on 1 procs for 58 steps with 1058 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 = -4617.13834551258 -4752.05576734712 -4752.06024464868 Force two-norm initial, final = 224.57797 0.22146385 Force max component initial, final = 54.544270 0.057201245 Final line search alpha, max atom move = 1.0000000 0.057201245 Iterations, force evaluations = 58 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6267 | 2.6267 | 2.6267 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02169 | 0.02169 | 0.02169 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01555 | | | 0.58 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8203.00 ave 8203 max 8203 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: 212276.0 ave 212276 max 212276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212276 Ave neighs/atom = 200.63894 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4752.0602 0 -4752.0602 23334.697 10864.043 65 0 -4752.7158 0 -4752.7158 -10.172649 10925.758 Loop time of 0.258243 on 1 procs for 7 steps with 1058 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 = -4752.06024464866 -4752.71201566161 -4752.71583142627 Force two-norm initial, final = 287.25834 0.45029641 Force max component initial, final = 228.41551 0.074540950 Final line search alpha, max atom move = 7.5693243e-05 5.6422462e-06 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24969 | 0.24969 | 0.24969 | 0.0 | 96.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019741 | 0.0019741 | 0.0019741 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006581 | | | 2.55 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8552.00 ave 8552 max 8552 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: 211300.0 ave 211300 max 211300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211300 Ave neighs/atom = 199.71645 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.600 | 5.600 | 5.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4752.7158 0 -4752.7158 -10.172649 Loop time of 7.227e-06 on 1 procs for 0 steps with 1058 atoms 207.6% 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 | | 7.227e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8566.00 ave 8566 max 8566 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: 211068.0 ave 211068 max 211068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211068 Ave neighs/atom = 199.49716 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.600 | 5.600 | 5.600 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 -4752.7158 -4752.7158 19.835085 112.853 4.8809505 -10.172649 -10.172649 -9.5644396 -10.026179 -10.927327 2.2619567 341.59541 Loop time of 8.5e-06 on 1 procs for 0 steps with 1058 atoms 188.2% 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 | | 8.5e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8566.00 ave 8566 max 8566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105534.0 ave 105534 max 105534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211068.0 ave 211068 max 211068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211068 Ave neighs/atom = 199.49716 Neighbor list builds = 0 Dangerous builds = 0 1058 -4752.71583142889 eV 2.26195667431376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03