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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -38.483858 0.0000000) to (27.212197 38.483858 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2062905 6.0763986 5.0973115 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.483858 0.0000000) to (27.212197 38.483858 5.0973115) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2062905 6.0763986 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.483858 0.0000000) to (27.212197 38.483858 5.0973115) create_atoms CPU = 0.001 seconds 458 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 = 10 26 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 2 atoms, new total = 912 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_492310898779_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 = 10 26 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3394.4542 0 -3394.4542 131580.63 468 0 -3883.3662 0 -3883.3662 -8175.5951 Loop time of 28.2106 on 1 procs for 468 steps with 912 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 = -3394.4542057167 -3883.36289993747 -3883.36618002121 Force two-norm initial, final = 1370.6036 0.17526053 Force max component initial, final = 460.19571 0.032972274 Final line search alpha, max atom move = 1.0000000 0.032972274 Iterations, force evaluations = 468 872 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.063 | 28.063 | 28.063 | 0.0 | 99.48 Neigh | 0.075889 | 0.075889 | 0.075889 | 0.0 | 0.27 Comm | 0.035791 | 0.035791 | 0.035791 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03615 | | | 0.13 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4163.00 ave 4163 max 4163 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: 60030.0 ave 60030 max 60030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60030 Ave neighs/atom = 65.822368 Neighbor list builds = 15 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 = 10 26 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 : 468 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 468 0 -3883.3662 0 -3883.3662 -8175.5951 10676.118 499 0 -3890.2844 0 -3890.2844 77.332138 10614.425 Loop time of 1.07473 on 1 procs for 31 steps with 912 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 = -3883.36618002121 -3890.28426145585 -3890.28437862156 Force two-norm initial, final = 427.02456 1.3746206 Force max component initial, final = 390.91699 0.86477305 Final line search alpha, max atom move = 0.00054227562 0.00046894534 Iterations, force evaluations = 31 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0673 | 1.0673 | 1.0673 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011935 | 0.0011935 | 0.0011935 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006254 | | | 0.58 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4162.00 ave 4162 max 4162 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: 60010.0 ave 60010 max 60010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60010 Ave neighs/atom = 65.800439 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 = 10 26 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) = 4.700 | 4.700 | 4.700 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3890.2844 0 -3890.2844 77.332138 Loop time of 2.196e-06 on 1 procs for 0 steps with 912 atoms 136.6% 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 | | 2.196e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4233.00 ave 4233 max 4233 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: 60010.0 ave 60010 max 60010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60010 Ave neighs/atom = 65.800439 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 = 10 26 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) = 4.700 | 4.700 | 4.700 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 -3890.2844 -3890.2844 27.586552 77.595573 4.9586344 77.332138 77.332138 132.32743 9.843022 89.825963 2.3095434 1699.402 Loop time of 1.639e-06 on 1 procs for 0 steps with 912 atoms 183.0% 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 | | 1.639e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4233.00 ave 4233 max 4233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30005.0 ave 30005 max 30005 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60010.0 ave 60010 max 60010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60010 Ave neighs/atom = 65.800439 Neighbor list builds = 0 Dangerous builds = 0 912 -3890.28437862156 eV 2.30954343071796 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29