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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -61.868815 0.0000000) to (30.932598 61.868815 3.6203867) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6610763 4.6610763 3.6203867 Created 585 atoms using lattice units in orthogonal box = (0.0000000 -61.868815 0.0000000) to (30.932598 61.868815 3.6203867) create_atoms CPU = 0.001 seconds 585 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6610763 4.6610763 3.6203867 Created 585 atoms using lattice units in orthogonal box = (0.0000000 -61.868815 0.0000000) to (30.932598 61.868815 3.6203867) create_atoms CPU = 0.001 seconds 585 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1152 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4056.9993 0 -4056.9993 -4713.8751 36 0 -4065.0186 0 -4065.0186 -12679.665 Loop time of 1.26033 on 1 procs for 36 steps with 1152 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 = -4056.9993362274 -4065.01487081445 -4065.01862379049 Force two-norm initial, final = 8.7913206 0.19477612 Force max component initial, final = 3.0947086 0.053288367 Final line search alpha, max atom move = 1.0000000 0.053288367 Iterations, force evaluations = 36 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2513 | 1.2513 | 1.2513 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043356 | 0.0043356 | 0.0043356 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004659 | | | 0.37 Nlocal: 1152.00 ave 1152 max 1152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5840.00 ave 5840 max 5840 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: 88650.0 ave 88650 max 88650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88650 Ave neighs/atom = 76.953125 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -4065.0186 0 -4065.0186 -12679.665 13857.125 43 0 -4065.4166 0 -4065.4166 -1906.0167 13750.02 Loop time of 0.191332 on 1 procs for 7 steps with 1152 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 = -4065.01862379049 -4065.41598972831 -4065.41659450367 Force two-norm initial, final = 140.49607 3.0195601 Force max component initial, final = 106.93478 2.9818180 Final line search alpha, max atom move = 0.00025015676 0.00074592194 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18841 | 0.18841 | 0.18841 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046506 | 0.00046506 | 0.00046506 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002455 | | | 1.28 Nlocal: 1152.00 ave 1152 max 1152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5872.00 ave 5872 max 5872 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: 89164.0 ave 89164 max 89164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89164 Ave neighs/atom = 77.399306 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.765 | 4.765 | 4.765 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4065.4166 0 -4065.4166 -1906.0167 Loop time of 2.03e-06 on 1 procs for 0 steps with 1152 atoms 197.0% 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 | | 2.03e-06 | | |100.00 Nlocal: 1152.00 ave 1152 max 1152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5872.00 ave 5872 max 5872 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: 89172.0 ave 89172 max 89172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89172 Ave neighs/atom = 77.406250 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.765 | 4.765 | 4.765 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 -4065.4166 -4065.4166 30.876928 123.73763 3.5988807 -1906.0167 -1906.0167 346.82137 -6106.9137 42.04225 2.3034468 499.75799 Loop time of 2.504e-06 on 1 procs for 0 steps with 1152 atoms 239.6% 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 | | 2.504e-06 | | |100.00 Nlocal: 1152.00 ave 1152 max 1152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5872.00 ave 5872 max 5872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44586.0 ave 44586 max 44586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89172.0 ave 89172 max 89172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89172 Ave neighs/atom = 77.406250 Neighbor list builds = 0 Dangerous builds = 0 1152 -4065.41659450367 eV 2.30344676277431 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01