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 = 4.0329885 4.0329885 4.0329885 Created orthogonal box = (0.0000000 -41.128574 0.0000000) to (20.564287 41.128574 4.0329885) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7456047 4.7456047 4.0329885 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.128574 0.0000000) to (20.564287 41.128574 4.0329885) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7456047 4.7456047 4.0329885 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.128574 0.0000000) to (20.564287 41.128574 4.0329885) create_atoms CPU = 0.000 seconds 210 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 12 1 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_140175748626_004#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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.349 | 5.349 | 5.349 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1161.6142 0 -1161.6142 7716.7208 46 0 -1194.6197 0 -1194.6197 -3003.6117 Loop time of 1.09958 on 1 procs for 46 steps with 412 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 = -1161.61420007669 -1194.61900125535 -1194.61966779728 Force two-norm initial, final = 61.285057 0.068577699 Force max component initial, final = 21.086796 0.014416766 Final line search alpha, max atom move = 1.0000000 0.014416766 Iterations, force evaluations = 46 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0757 | 1.0757 | 1.0757 | 0.0 | 97.83 Neigh | 0.014291 | 0.014291 | 0.014291 | 0.0 | 1.30 Comm | 0.0065835 | 0.0065835 | 0.0065835 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002969 | | | 0.27 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9203.00 ave 9203 max 9203 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: 272328.0 ave 272328 max 272328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272328 Ave neighs/atom = 660.99029 Neighbor list builds = 1 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.349 | 5.349 | 5.349 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1194.6197 0 -1194.6197 -3003.6117 6822.0405 53 0 -1194.6797 0 -1194.6797 -214.66275 6796.0069 Loop time of 0.118208 on 1 procs for 7 steps with 412 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 = -1194.61966779728 -1194.6792659354 -1194.67970695379 Force two-norm initial, final = 23.844353 1.8578935 Force max component initial, final = 16.510014 1.3321828 Final line search alpha, max atom move = 0.00058046391 0.00077328406 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11551 | 0.11551 | 0.11551 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057843 | 0.00057843 | 0.00057843 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002121 | | | 1.79 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9200.00 ave 9200 max 9200 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: 274088.0 ave 274088 max 274088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274088 Ave neighs/atom = 665.26214 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.487 | 5.487 | 5.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1194.6797 0 -1194.6797 -214.66275 Loop time of 1.909e-06 on 1 procs for 0 steps with 412 atoms 157.2% 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 | | 1.909e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9235.00 ave 9235 max 9235 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: 274536.0 ave 274536 max 274536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274536 Ave neighs/atom = 666.34951 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.487 | 5.487 | 5.487 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 -1194.6797 -1194.6797 20.480031 81.928722 4.0502985 -214.66275 -214.66275 -312.77881 -297.15266 -34.056784 2.5518141 261.97394 Loop time of 2.468e-06 on 1 procs for 0 steps with 412 atoms 243.1% 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 | | 2.468e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9235.00 ave 9235 max 9235 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137268.0 ave 137268 max 137268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274536.0 ave 274536 max 274536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274536 Ave neighs/atom = 666.34951 Neighbor list builds = 0 Dangerous builds = 0 412 -1194.67970695379 eV 2.55181412332676 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01