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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -61.112400 0.0000000) to (43.210131 61.112400 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8226523 5.8964201 5.7233217 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.112400 0.0000000) to (43.210131 61.112400 5.7233217) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8226523 5.8964201 5.7233217 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.112400 0.0000000) to (43.210131 61.112400 5.7233217) create_atoms CPU = 0.002 seconds 916 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 35 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1808 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.162 | 5.162 | 5.162 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6010.4768 0 -6010.4768 4495.7024 52 0 -6063.4829 0 -6063.4829 -4716.9939 Loop time of 6.89243 on 1 procs for 52 steps with 1808 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6010.47682858179 -6063.47762650388 -6063.48289138952 Force two-norm initial, final = 38.126449 0.21657405 Force max component initial, final = 6.6269999 0.036839831 Final line search alpha, max atom move = 1.0000000 0.036839831 Iterations, force evaluations = 52 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8642 | 6.8642 | 6.8642 | 0.0 | 99.59 Neigh | 0.010774 | 0.010774 | 0.010774 | 0.0 | 0.16 Comm | 0.0088301 | 0.0088301 | 0.0088301 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008664 | | | 0.13 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7551.00 ave 7551 max 7551 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: 154080.0 ave 154080 max 154080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154080 Ave neighs/atom = 85.221239 Neighbor list builds = 1 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.162 | 5.162 | 5.162 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -6063.4829 0 -6063.4829 -4716.9939 30226.863 56 0 -6063.6508 0 -6063.6508 -1269.772 30092.43 Loop time of 0.537601 on 1 procs for 4 steps with 1808 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 = -6063.48289138951 -6063.64978588804 -6063.65077186947 Force two-norm initial, final = 104.01434 0.23498825 Force max component initial, final = 79.650218 0.032290367 Final line search alpha, max atom move = 0.00027096475 8.7495513e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53521 | 0.53521 | 0.53521 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040523 | 0.00040523 | 0.00040523 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001982 | | | 0.37 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7572.00 ave 7572 max 7572 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: 154624.0 ave 154624 max 154624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154624 Ave neighs/atom = 85.522124 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.300 | 5.300 | 5.300 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6063.6508 0 -6063.6508 -1269.772 Loop time of 1.812e-06 on 1 procs for 0 steps with 1808 atoms 165.6% 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 | | 1.812e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7579.00 ave 7579 max 7579 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: 154792.0 ave 154792 max 154792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154792 Ave neighs/atom = 85.615044 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.300 | 5.300 | 5.300 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 -6063.6508 -6063.6508 43.085805 122.2248 5.7143088 -1269.772 -1269.772 -0.25118303 -3807.4187 -1.6461434 2.484866 1115.4458 Loop time of 2.025e-06 on 1 procs for 0 steps with 1808 atoms 197.5% 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 | | 2.025e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7579.00 ave 7579 max 7579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77396.0 ave 77396 max 77396 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154792.0 ave 154792 max 154792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154792 Ave neighs/atom = 85.615044 Neighbor list builds = 0 Dangerous builds = 0 1808 -6063.65077186947 eV 2.48486597965336 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08