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 = 3.6150004 3.6150004 3.6150004 Created orthogonal box = (0.0000000 -36.509714 0.0000000) to (25.816266 36.509714 5.1123825) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5558117 5.7270140 5.1123825 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.509714 0.0000000) to (25.816266 36.509714 5.1123825) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5558117 5.7270140 5.1123825 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.509714 0.0000000) to (25.816266 36.509714 5.1123825) create_atoms CPU = 0.001 seconds 410 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 23 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 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_762798677854_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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2596.6088 0 -2596.6088 118852.47 39 0 -2840.7541 0 -2840.7541 6113.9372 Loop time of 0.231014 on 1 procs for 39 steps with 812 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 = -2596.60881362117 -2840.75192416897 -2840.75405764538 Force two-norm initial, final = 1333.1658 0.12151005 Force max component initial, final = 457.09079 0.013361322 Final line search alpha, max atom move = 1.0000000 0.013361322 Iterations, force evaluations = 39 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21461 | 0.21461 | 0.21461 | 0.0 | 92.90 Neigh | 0.011188 | 0.011188 | 0.011188 | 0.0 | 4.84 Comm | 0.0026051 | 0.0026051 | 0.0026051 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002608 | | | 1.13 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4169.00 ave 4169 max 4169 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: 69508.0 ave 69508 max 69508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69508 Ave neighs/atom = 85.600985 Neighbor list builds = 2 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -2840.7541 0 -2840.7541 6113.9372 9637.2961 44 0 -2840.8871 0 -2840.8871 -23.723446 9676.1828 Loop time of 0.0290527 on 1 procs for 5 steps with 812 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 = -2840.75405764538 -2840.88696303035 -2840.887108979 Force two-norm initial, final = 73.032409 0.75093855 Force max component initial, final = 63.361714 0.68758239 Final line search alpha, max atom move = 0.00043839711 0.00030143413 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027309 | 0.027309 | 0.027309 | 0.0 | 94.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028219 | 0.00028219 | 0.00028219 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001462 | | | 5.03 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4213.00 ave 4213 max 4213 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: 69544.0 ave 69544 max 69544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69544 Ave neighs/atom = 85.645320 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2840.8871 0 -2840.8871 -23.723446 Loop time of 1.736e-06 on 1 procs for 0 steps with 812 atoms 172.8% 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 | | 1.736e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4226.00 ave 4226 max 4226 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: 69488.0 ave 69488 max 69488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69488 Ave neighs/atom = 85.576355 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.686 | 4.686 | 4.686 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 -2840.8871 -2840.8871 25.841046 73.306071 5.1080369 -23.723446 -23.723446 -113.95876 6.5166495 36.27177 2.2297883 406.58375 Loop time of 2.253e-06 on 1 procs for 0 steps with 812 atoms 177.5% 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 | | 2.253e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4226.00 ave 4226 max 4226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34744.0 ave 34744 max 34744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69488.0 ave 69488 max 69488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69488 Ave neighs/atom = 85.576355 Neighbor list builds = 0 Dangerous builds = 0 812 -2840.887108979 eV 2.22978834833627 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00