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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -42.112915 0.0000000) to (14.889164 42.112915 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1308321 6.1930757 5.1069410 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.112915 0.0000000) to (14.889164 42.112915 5.1069410) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1308321 6.1930757 5.1069410 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.112915 0.0000000) to (14.889164 42.112915 5.1069410) create_atoms CPU = 0.001 seconds 274 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.868 | 4.868 | 4.868 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2213.6599 0 -2213.6599 32378.02 102 0 -2304.6521 0 -2304.6521 3368.5747 Loop time of 5.57794 on 1 procs for 102 steps with 544 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 = -2213.65985830171 -2304.65036335787 -2304.65212438017 Force two-norm initial, final = 181.71918 0.18355909 Force max component initial, final = 63.017456 0.028017794 Final line search alpha, max atom move = 1.0000000 0.028017794 Iterations, force evaluations = 102 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5638 | 5.5638 | 5.5638 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0070646 | 0.0070646 | 0.0070646 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007075 | | | 0.13 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2926.00 ave 2926 max 2926 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: 29404.0 ave 29404 max 29404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29404 Ave neighs/atom = 54.051471 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.866 | 4.866 | 4.866 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -2304.6521 0 -2304.6521 3368.5747 6404.3704 104 0 -2304.666 0 -2304.666 -2.8220553 6417.3693 Loop time of 0.134513 on 1 procs for 2 steps with 544 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 = -2304.65212438017 -2304.66591933665 -2304.66604114166 Force two-norm initial, final = 23.407250 0.20920682 Force max component initial, final = 14.826198 0.066233186 Final line search alpha, max atom move = 0.0010225145 6.7724392e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13376 | 0.13376 | 0.13376 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012189 | 0.00012189 | 0.00012189 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006365 | | | 0.47 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 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: 29408.0 ave 29408 max 29408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29408 Ave neighs/atom = 54.058824 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2304.666 0 -2304.666 -2.8220553 Loop time of 1.98e-06 on 1 procs for 0 steps with 544 atoms 151.5% 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 | | 1.98e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 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: 29408.0 ave 29408 max 29408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29408 Ave neighs/atom = 54.058824 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.004 | 5.004 | 5.004 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 -2304.666 -2304.666 14.902059 84.284836 5.1092989 -2.8220553 -2.8220553 -16.550265 12.844771 -4.7606721 2.3375789 250.01622 Loop time of 1.627e-06 on 1 procs for 0 steps with 544 atoms 122.9% 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 | | 1.627e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14704.0 ave 14704 max 14704 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29408.0 ave 29408 max 29408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29408 Ave neighs/atom = 54.058824 Neighbor list builds = 0 Dangerous builds = 0 544 -2304.66604114166 eV 2.33757885478317 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06