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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.575781 0.0000000) to (40.746946 70.575781 6.0968189) create_atoms CPU = 0.004 seconds 1610 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 34 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.76 | 11.76 | 11.76 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14170.27 0 -14170.27 3592.8998 97 0 -14268.204 0 -14268.204 6160.0333 Loop time of 6.41946 on 1 procs for 97 steps with 3216 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14170.2695715087 -14268.1914060912 -14268.2044373607 Force two-norm initial, final = 36.970593 0.37076386 Force max component initial, final = 5.1925148 0.041894459 Final line search alpha, max atom move = 1.0000000 0.041894459 Iterations, force evaluations = 97 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2068 | 6.2068 | 6.2068 | 0.0 | 96.69 Neigh | 0.13866 | 0.13866 | 0.13866 | 0.0 | 2.16 Comm | 0.040674 | 0.040674 | 0.040674 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03337 | | | 0.52 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17180.0 ave 17180 max 17180 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: 720596.0 ave 720596 max 720596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720596 Ave neighs/atom = 224.06592 Neighbor list builds = 3 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -14268.204 0 -14268.204 6160.0333 35065.824 102 0 -14268.776 0 -14268.776 30.213944 35186.151 Loop time of 0.240504 on 1 procs for 5 steps with 3216 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 = -14268.204437361 -14268.7746057332 -14268.7761412712 Force two-norm initial, final = 296.26403 1.2578726 Force max component initial, final = 277.01578 0.72166369 Final line search alpha, max atom move = 0.00011858417 8.5577890e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23512 | 0.23512 | 0.23512 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095468 | 0.00095468 | 0.00095468 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004425 | | | 1.84 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17196.0 ave 17196 max 17196 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: 720660.0 ave 720660 max 720660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720660 Ave neighs/atom = 224.08582 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.28 | 11.28 | 11.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14268.776 0 -14268.776 30.213944 Loop time of 2.103e-06 on 1 procs for 0 steps with 3216 atoms 190.2% 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 | | 2.103e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17196.0 ave 17196 max 17196 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: 720184.0 ave 720184 max 720184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720184 Ave neighs/atom = 223.93781 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 11.28 | 11.28 | 11.28 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 -14268.776 -14268.776 40.751076 141.74169 6.0916517 30.213944 30.213944 29.926353 32.997829 27.717651 2.2013379 996.93078 Loop time of 2.335e-06 on 1 procs for 0 steps with 3216 atoms 299.8% 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 | | 2.335e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17196.0 ave 17196 max 17196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 360092.0 ave 360092 max 360092 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 720184.0 ave 720184 max 720184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720184 Ave neighs/atom = 223.93781 Neighbor list builds = 0 Dangerous builds = 0 3216 -14268.7761412712 eV 2.20133790644781 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07