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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -70.376612 0.0000000) to (40.629832 70.376612 6.3712660) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9945654 5.3837217 6.3712660 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -70.376612 0.0000000) to (40.629832 70.376612 6.3712660) create_atoms CPU = 0.008 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9945654 5.3837217 6.3712660 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -70.376612 0.0000000) to (40.629832 70.376612 6.3712660) create_atoms CPU = 0.007 seconds 1466 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 3 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2900 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.782 | 5.782 | 5.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12166.417 0 -12166.417 1040.3134 463 0 -12259.938 0 -12259.938 -61123.86 Loop time of 17.3153 on 1 procs for 463 steps with 2900 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 = -12166.4173609836 -12259.9255606936 -12259.9377949297 Force two-norm initial, final = 35.547483 0.39487919 Force max component initial, final = 8.3511696 0.064561607 Final line search alpha, max atom move = 1.0000000 0.064561607 Iterations, force evaluations = 463 855 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.341 | 16.341 | 16.341 | 0.0 | 94.37 Neigh | 0.54328 | 0.54328 | 0.54328 | 0.0 | 3.14 Comm | 0.18489 | 0.18489 | 0.18489 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2464 | | | 1.42 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9208.00 ave 9208 max 9208 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: 193888.0 ave 193888 max 193888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193888 Ave neighs/atom = 66.857931 Neighbor list builds = 15 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 463 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 463 0 -12259.938 0 -12259.938 -61123.86 36435.868 488 0 -12285.203 0 -12285.203 -12709.394 35145.426 Loop time of 0.618212 on 1 procs for 25 steps with 2900 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12259.9377949295 -12285.1990494256 -12285.2034750356 Force two-norm initial, final = 1857.6598 6.8129291 Force max component initial, final = 1506.6687 5.4139812 Final line search alpha, max atom move = 5.3789538e-05 0.00029121554 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58219 | 0.58219 | 0.58219 | 0.0 | 94.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0060313 | 0.0060313 | 0.0060313 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02999 | | | 4.85 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9205.00 ave 9205 max 9205 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: 193880.0 ave 193880 max 193880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193880 Ave neighs/atom = 66.855172 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.918 | 5.918 | 5.918 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12285.203 0 -12285.203 -12709.394 Loop time of 8.36e-06 on 1 procs for 0 steps with 2900 atoms 179.4% 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 | | 8.36e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9410.00 ave 9410 max 9410 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: 200240.0 ave 200240 max 200240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200240 Ave neighs/atom = 69.048276 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 13 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.918 | 5.918 | 5.918 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 -12285.203 -12285.203 39.648017 140.75322 6.297802 -12709.394 -12709.394 -240.84338 -37762.14 -125.19879 2.2405405 3331.7957 Loop time of 7.267e-06 on 1 procs for 0 steps with 2900 atoms 289.0% 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 | | 7.267e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9410.00 ave 9410 max 9410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100120.0 ave 100120 max 100120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200240.0 ave 200240 max 200240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200240 Ave neighs/atom = 69.048276 Neighbor list builds = 0 Dangerous builds = 0 2900 -12285.2031850356 eV 2.24054045501283 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18