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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -42.182596 0.0000000) to (34.439618 42.182596 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2459803 4.0446331 4.6544275 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.182596 0.0000000) to (34.439618 42.182596 6.9816412) create_atoms CPU = 0.001 seconds 877 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2459803 4.0446331 4.6544275 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.182596 0.0000000) to (34.439618 42.182596 6.9816412) create_atoms CPU = 0.001 seconds 877 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1736 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_304347095149_000#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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.107 | 5.107 | 5.107 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7303.8886 0 -7303.8886 14932.505 139 0 -7412.5255 0 -7412.5255 -7841.1586 Loop time of 25.025 on 1 procs for 139 steps with 1736 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 = -7303.88856935819 -7412.51837067274 -7412.52548143732 Force two-norm initial, final = 136.95039 0.25471629 Force max component initial, final = 26.509129 0.055923748 Final line search alpha, max atom move = 1.0000000 0.055923748 Iterations, force evaluations = 139 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.958 | 24.958 | 24.958 | 0.0 | 99.73 Neigh | 0.031715 | 0.031715 | 0.031715 | 0.0 | 0.13 Comm | 0.013917 | 0.013917 | 0.013917 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02108 | | | 0.08 Nlocal: 1736.00 ave 1736 max 1736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5862.00 ave 5862 max 5862 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: 113586.0 ave 113586 max 113586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113586 Ave neighs/atom = 65.429724 Neighbor list builds = 3 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 139 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.107 | 5.107 | 5.107 Mbytes Step Temp E_pair E_mol TotEng Press Volume 139 0 -7412.5255 0 -7412.5255 -7841.1586 20285.193 143 0 -7412.7927 0 -7412.7927 -134.27771 20189.866 Loop time of 0.674682 on 1 procs for 4 steps with 1736 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 = -7412.52548143729 -7412.79214417661 -7412.79266374207 Force two-norm initial, final = 159.35833 0.30218537 Force max component initial, final = 115.98617 0.056033928 Final line search alpha, max atom move = 0.00027392199 1.5348925e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67254 | 0.67254 | 0.67254 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030538 | 0.00030538 | 0.00030538 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001834 | | | 0.27 Nlocal: 1736.00 ave 1736 max 1736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5873.00 ave 5873 max 5873 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: 113486.0 ave 113486 max 113486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113486 Ave neighs/atom = 65.372120 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7412.7927 0 -7412.7927 -134.27771 Loop time of 1.681e-06 on 1 procs for 0 steps with 1736 atoms 178.5% 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 | | 1.681e-06 | | |100.00 Nlocal: 1736.00 ave 1736 max 1736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5876.00 ave 5876 max 5876 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: 113700.0 ave 113700 max 113700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113700 Ave neighs/atom = 65.495392 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.245 | 5.245 | 5.245 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 -7412.7927 -7412.7927 34.346661 84.365192 6.9676386 -134.27771 -134.27771 -1.7550873 -396.83541 -4.2426215 2.2548426 1131.0099 Loop time of 1.615e-06 on 1 procs for 0 steps with 1736 atoms 185.8% 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 | | 1.615e-06 | | |100.00 Nlocal: 1736.00 ave 1736 max 1736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5876.00 ave 5876 max 5876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56850.0 ave 56850 max 56850 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113700.0 ave 113700 max 113700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113700 Ave neighs/atom = 65.495392 Neighbor list builds = 0 Dangerous builds = 0 1736 -7412.79266374207 eV 2.25484257616775 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26