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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -35.182745 0.0000000) to (7.0359197 35.182745 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2215518 4.2215518 3.1465590 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -35.182745 0.0000000) to (7.0359197 35.182745 3.1465590) create_atoms CPU = 0.001 seconds 51 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2215518 4.2215518 3.1465590 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -35.182745 0.0000000) to (7.0359197 35.182745 3.1465590) create_atoms CPU = 0.000 seconds 51 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 3 25 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 98 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.359 | 4.359 | 4.359 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -659.45036 0 -659.45036 -19330.024 15 0 -662.18533 0 -662.18533 -36286.883 Loop time of 0.181572 on 1 procs for 15 steps with 98 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -659.450360591722 -662.184862971367 -662.185332552221 Force two-norm initial, final = 3.1265832 0.058338517 Force max component initial, final = 1.0811201 0.013753847 Final line search alpha, max atom move = 1.0000000 0.013753847 Iterations, force evaluations = 15 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18011 | 0.18011 | 0.18011 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078283 | 0.00078283 | 0.00078283 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006813 | | | 0.38 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1271.00 ave 1271 max 1271 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: 5540.00 ave 5540 max 5540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5540 Ave neighs/atom = 56.530612 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.359 | 4.359 | 4.359 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -662.18533 0 -662.18533 -36286.883 1557.8171 23 0 -662.36863 0 -662.36863 -8279.1802 1540.5709 Loop time of 0.0718 on 1 procs for 8 steps with 98 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -662.185332552221 -662.368499229478 -662.368626981753 Force two-norm initial, final = 45.260727 0.11838757 Force max component initial, final = 35.921859 0.046945631 Final line search alpha, max atom move = 0.0013578460 6.3744936e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07049 | 0.07049 | 0.07049 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029692 | 0.00029692 | 0.00029692 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001013 | | | 1.41 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1271.00 ave 1271 max 1271 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: 5596.00 ave 5596 max 5596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5596 Ave neighs/atom = 57.102041 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -662.36863 0 -662.36863 -8279.1802 Loop time of 6.415e-06 on 1 procs for 0 steps with 98 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1271.00 ave 1271 max 1271 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: 5596.00 ave 5596 max 5596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5596 Ave neighs/atom = 57.102041 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.497 | 4.497 | 4.497 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 -662.36863 -662.36863 7.0062453 70.36549 3.1249037 -8279.1802 -8279.1802 -17.723407 -24826.2 6.3828158 2.5151178 79.86146 Loop time of 6.605e-06 on 1 procs for 0 steps with 98 atoms 166.5% 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 | | 6.605e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1271.00 ave 1271 max 1271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2798.00 ave 2798 max 2798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5596.00 ave 5596 max 5596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5596 Ave neighs/atom = 57.102041 Neighbor list builds = 0 Dangerous builds = 0 98 -662.368626981753 eV 2.51511777276429 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00