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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -41.626971 0.0000000) to (50.982419 41.626971 8.6176017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8265622 5.3520391 5.7450678 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -41.626971 0.0000000) to (50.982419 41.626971 8.6176017) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8265622 5.3520391 5.7450678 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.626971 0.0000000) to (50.982419 41.626971 8.6176017) create_atoms CPU = 0.002 seconds 1687 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 13 21 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3350 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_832600236922_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.399 | 7.399 | 7.399 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13499.693 0 -13499.693 103894.71 119 0 -14626.393 0 -14626.393 2568.6413 Loop time of 6.19475 on 1 procs for 119 steps with 3350 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13499.6930912318 -14626.3780297424 -14626.3926132957 Force two-norm initial, final = 1320.2298 0.41295733 Force max component initial, final = 235.39978 0.065466498 Final line search alpha, max atom move = 0.95282374 0.062378033 Iterations, force evaluations = 119 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8415 | 5.8415 | 5.8415 | 0.0 | 94.30 Neigh | 0.28369 | 0.28369 | 0.28369 | 0.0 | 4.58 Comm | 0.028834 | 0.028834 | 0.028834 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04068 | | | 0.66 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11722.0 ave 11722 max 11722 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: 663882.0 ave 663882 max 663882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663882 Ave neighs/atom = 198.17373 Neighbor list builds = 7 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -14626.393 0 -14626.393 2568.6413 36577.301 122 0 -14626.501 0 -14626.501 36.8921 36632.739 Loop time of 0.183812 on 1 procs for 3 steps with 3350 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 = -14626.3926132957 -14626.5011442234 -14626.501263238 Force two-norm initial, final = 125.70248 1.6692433 Force max component initial, final = 118.15121 1.3120628 Final line search alpha, max atom move = 0.00027344133 0.00035877219 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17998 | 0.17998 | 0.17998 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056452 | 0.00056452 | 0.00056452 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003266 | | | 1.78 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11768.0 ave 11768 max 11768 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: 663930.0 ave 663930 max 663930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663930 Ave neighs/atom = 198.18806 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.539 | 7.539 | 7.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14626.501 0 -14626.501 36.8921 Loop time of 2.162e-06 on 1 procs for 0 steps with 3350 atoms 231.3% 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 | | 2.162e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11770.0 ave 11770 max 11770 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: 663444.0 ave 663444 max 663444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663444 Ave neighs/atom = 198.04299 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.539 | 7.539 | 7.539 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 -14626.501 -14626.501 50.965158 83.412648 8.617159 36.8921 36.8921 57.365202 37.630087 15.681012 2.1852112 1628.736 Loop time of 2.949e-06 on 1 procs for 0 steps with 3350 atoms 203.5% 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 | | 2.949e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11770.0 ave 11770 max 11770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 331722.0 ave 331722 max 331722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 663444.0 ave 663444 max 663444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663444 Ave neighs/atom = 198.04299 Neighbor list builds = 0 Dangerous builds = 0 3350 -14626.501263238 eV 2.18521119314657 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07