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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -44.125349 0.0000000) to (14.708450 44.125349 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3260146 4.3260146 3.5673230 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.125349 0.0000000) to (14.708450 44.125349 3.5673230) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3260146 4.3260146 3.5673230 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.125349 0.0000000) to (14.708450 44.125349 3.5673230) create_atoms CPU = 0.000 seconds 206 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, 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, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1654.863 0 -1654.863 42237.878 60 0 -1716.315 0 -1716.315 32671.98 Loop time of 1.38502 on 1 procs for 60 steps with 408 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 = -1654.86303058822 -1716.31497704028 -1716.31500404881 Force two-norm initial, final = 152.77651 0.88376172 Force max component initial, final = 51.917257 0.34788702 Final line search alpha, max atom move = 0.58592615 0.20383611 Iterations, force evaluations = 60 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3758 | 1.3758 | 1.3758 | 0.0 | 99.33 Neigh | 0.0021121 | 0.0021121 | 0.0021121 | 0.0 | 0.15 Comm | 0.0037049 | 0.0037049 | 0.0037049 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00344 | | | 0.25 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2816.00 ave 2816 max 2816 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: 23088.0 ave 23088 max 23088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23088 Ave neighs/atom = 56.588235 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1716.315 0 -1716.315 32671.98 4630.4956 115 0 -1719.3777 0 -1719.3777 -102.71625 4774.2458 Loop time of 0.705826 on 1 procs for 55 steps with 408 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 = -1716.31500404881 -1719.37683243165 -1719.37767791028 Force two-norm initial, final = 179.02572 1.8564567 Force max component initial, final = 146.49642 1.1327603 Final line search alpha, max atom move = 0.00067120212 0.00076031109 Iterations, force evaluations = 55 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68806 | 0.68806 | 0.68806 | 0.0 | 97.48 Neigh | 0.0083373 | 0.0083373 | 0.0083373 | 0.0 | 1.18 Comm | 0.0017937 | 0.0017937 | 0.0017937 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007631 | | | 1.08 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 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: 24456.0 ave 24456 max 24456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24456 Ave neighs/atom = 59.941176 Neighbor list builds = 4 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1719.3777 0 -1719.3777 -102.71625 Loop time of 2.317e-06 on 1 procs for 0 steps with 408 atoms 172.6% 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 | | 2.317e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 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: 24004.0 ave 24004 max 24004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24004 Ave neighs/atom = 58.833333 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.584 | 4.584 | 4.584 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 -1719.3777 -1719.3777 14.614747 92.290643 3.5396133 -102.71625 -102.71625 193.05222 -397.54209 -103.6589 2.3504699 200.70568 Loop time of 1.875e-06 on 1 procs for 0 steps with 408 atoms 213.3% 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 | | 1.875e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2824.00 ave 2824 max 2824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12002.0 ave 12002 max 12002 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24004.0 ave 24004 max 24004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24004 Ave neighs/atom = 58.833333 Neighbor list builds = 0 Dangerous builds = 0 408 -1719.37767791028 eV 2.35046985399074 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02