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 = 4.1768978 4.1768978 4.1768978 Created orthogonal box = (0.0000000 -49.421721 0.0000000) to (60.529000 49.421721 10.231268) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9176000 6.3542213 6.8208456 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -49.421721 0.0000000) to (60.529000 49.421721 10.231268) create_atoms CPU = 0.002 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9176000 6.3542213 6.8208456 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -49.421721 0.0000000) to (60.529000 49.421721 10.231268) create_atoms CPU = 0.002 seconds 1690 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 19 30 4 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3352 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 19 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.198 | 5.198 | 5.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -24061.9 0 -24061.9 27197.071 295 0 -24682.073 0 -24682.073 -601.88145 Loop time of 54.8661 on 1 procs for 295 steps with 3352 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -24061.9001771732 -24682.0489324345 -24682.0729242201 Force two-norm initial, final = 281.52635 0.59226908 Force max component initial, final = 27.104772 0.12859756 Final line search alpha, max atom move = 0.59236690 0.076176938 Iterations, force evaluations = 295 544 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 54.564 | 54.564 | 54.564 | 0.0 | 99.45 Neigh | 0.16244 | 0.16244 | 0.16244 | 0.0 | 0.30 Comm | 0.05006 | 0.05006 | 0.05006 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08938 | | | 0.16 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7252.00 ave 7252 max 7252 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: 215642.0 ave 215642 max 215642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215642 Ave neighs/atom = 64.332339 Neighbor list builds = 9 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 19 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 295 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 295 0 -24682.073 0 -24682.073 -601.88145 61212.601 307 0 -24688.013 0 -24688.013 -1.8289155 61183.933 Loop time of 1.37648 on 1 procs for 12 steps with 3352 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 = -24682.0729242201 -24688.012346072 -24688.0130394892 Force two-norm initial, final = 857.68244 1.7442064 Force max component initial, final = 704.09713 0.55788438 Final line search alpha, max atom move = 0.00015652110 8.7320677e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3695 | 1.3695 | 1.3695 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077132 | 0.00077132 | 0.00077132 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006203 | | | 0.45 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7251.00 ave 7251 max 7251 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: 215634.0 ave 215634 max 215634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215634 Ave neighs/atom = 64.329952 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.719 | 5.719 | 5.719 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -24688.013 0 -24688.013 -1.8289155 Loop time of 2.217e-06 on 1 procs for 0 steps with 3352 atoms 225.5% 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 | | 2.217e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7239.00 ave 7239 max 7239 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: 215568.0 ave 215568 max 215568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215568 Ave neighs/atom = 64.310263 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.719 | 5.719 | 5.719 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 -24688.013 -24688.013 59.856815 99.141544 10.310224 -1.8289155 -1.8289155 10.121898 -14.652947 -0.95569738 2.5893893 8373.5755 Loop time of 2.231e-06 on 1 procs for 0 steps with 3352 atoms 224.1% 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 | | 2.231e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7239.00 ave 7239 max 7239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107784.0 ave 107784 max 107784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215568.0 ave 215568 max 215568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215568 Ave neighs/atom = 64.310263 Neighbor list builds = 0 Dangerous builds = 0 3352 -24688.0130394891 eV 2.58938931082831 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:57