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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -41.933427 0.0000000) to (13.977809 41.933427 3.3901167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1111203 4.1111203 3.3901167 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -41.933427 0.0000000) to (13.977809 41.933427 3.3901167) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1111203 4.1111203 3.3901167 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -41.933427 0.0000000) to (13.977809 41.933427 3.3901167) create_atoms CPU = 0.000 seconds 103 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 205 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 5.809 | 5.809 | 5.809 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 3543.4597 0 3543.4597 18421427 78 0 -7272.8165 0 -7272.8165 258463.36 Loop time of 0.693465 on 1 procs for 78 steps with 205 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 3543.45974181666 -7272.8099586579 -7272.81654628154 Force two-norm initial, final = 52759.042 1.3303327 Force max component initial, final = 27831.485 0.47832154 Final line search alpha, max atom move = 0.16071941 0.076875553 Iterations, force evaluations = 78 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6695 | 0.6695 | 0.6695 | 0.0 | 96.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018702 | 0.018702 | 0.018702 | 0.0 | 2.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005263 | | | 0.76 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15369.0 ave 15369 max 15369 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: 379336.0 ave 379336 max 379336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379336 Ave neighs/atom = 1850.4195 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.814 | 5.814 | 5.814 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -7272.8165 0 -7272.8165 258463.36 3974.1486 722 0 -7530.9654 0 -7530.9654 -869.29048 3937.394 Loop time of 4.41994 on 1 procs for 644 steps with 205 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 = -7272.81654628156 -7530.95902329228 -7530.96535228274 Force two-norm initial, final = 1715.9192 23.054348 Force max component initial, final = 1182.0723 11.684988 Final line search alpha, max atom move = 7.1824296e-05 0.00083926607 Iterations, force evaluations = 644 799 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8618 | 3.8618 | 3.8618 | 0.0 | 87.37 Neigh | 0.079486 | 0.079486 | 0.079486 | 0.0 | 1.80 Comm | 0.098847 | 0.098847 | 0.098847 | 0.0 | 2.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3798 | | | 8.59 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15895.0 ave 15895 max 15895 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: 384950.0 ave 384950 max 384950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384950 Ave neighs/atom = 1877.8049 Neighbor list builds = 5 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 9.076 | 9.076 | 9.076 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7530.9654 0 -7530.9654 -869.29048 Loop time of 2.236e-06 on 1 procs for 0 steps with 205 atoms 134.2% 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 | | 2.236e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15958.0 ave 15958 max 15958 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: 385732.0 ave 385732 max 385732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 385732 Ave neighs/atom = 1881.6195 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 2 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 9.076 | 9.076 | 9.076 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 -7530.9654 -7530.9654 15.431709 84.909665 3.0049533 -869.29048 -869.29048 -1620.0894 -4813.8942 3826.1121 2.8285317 1147.9422 Loop time of 3.025e-06 on 1 procs for 0 steps with 205 atoms 231.4% 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 | | 3.025e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15958.0 ave 15958 max 15958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 192866.0 ave 192866 max 192866 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 385732.0 ave 385732 max 385732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 385732 Ave neighs/atom = 1881.6195 Neighbor list builds = 0 Dangerous builds = 0 205 -7530.96535228274 eV 2.82853171271846 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05