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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -34.719860 0.0000000) to (28.348647 34.719860 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0498067 4.0152219 4.6763140 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.719860 0.0000000) to (28.348647 34.719860 7.0144710) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0498067 4.0152219 4.6763140 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.719860 0.0000000) to (28.348647 34.719860 7.0144710) create_atoms CPU = 0.001 seconds 590 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 22 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1172 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4413.6931 0 -4413.6931 82381.946 63 0 -4996.196 0 -4996.196 5010.7436 Loop time of 9.85922 on 1 procs for 63 steps with 1172 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 = -4413.69306624776 -4996.19195510787 -4996.19597635934 Force two-norm initial, final = 860.72571 0.19589364 Force max component initial, final = 255.35889 0.021757154 Final line search alpha, max atom move = 1.0000000 0.021757154 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8274 | 9.8274 | 9.8274 | 0.0 | 99.68 Neigh | 0.018372 | 0.018372 | 0.018372 | 0.0 | 0.19 Comm | 0.0054181 | 0.0054181 | 0.0054181 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008001 | | | 0.08 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4534.00 ave 4534 max 4534 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: 116612.0 ave 116612 max 116612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116612 Ave neighs/atom = 99.498294 Neighbor list builds = 2 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4996.196 0 -4996.196 5010.7436 13808.141 70 0 -4996.5635 0 -4996.5635 -75.271379 13848.463 Loop time of 0.849561 on 1 procs for 7 steps with 1172 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 = -4996.19597635933 -4996.56116415397 -4996.56348419637 Force two-norm initial, final = 118.77898 1.2579082 Force max component initial, final = 117.38416 0.83785076 Final line search alpha, max atom move = 0.00016754432 0.00014037714 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8469 | 0.8469 | 0.8469 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035478 | 0.00035478 | 0.00035478 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002305 | | | 0.27 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4506.00 ave 4506 max 4506 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: 116684.0 ave 116684 max 116684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116684 Ave neighs/atom = 99.559727 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.145 | 5.145 | 5.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4996.5635 0 -4996.5635 -75.271379 Loop time of 2.435e-06 on 1 procs for 0 steps with 1172 atoms 123.2% 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 | | 2.435e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4506.00 ave 4506 max 4506 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: 117120.0 ave 117120 max 117120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117120 Ave neighs/atom = 99.931741 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.145 | 5.145 | 5.145 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 -4996.5635 -4996.5635 28.30166 69.890105 7.0012238 -75.271379 -75.271379 -96.773185 -83.743091 -45.297862 2.3099186 1208.4503 Loop time of 2.317e-06 on 1 procs for 0 steps with 1172 atoms 215.8% 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 | | 2.317e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4506.00 ave 4506 max 4506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58560.0 ave 58560 max 58560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117120.0 ave 117120 max 117120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117120 Ave neighs/atom = 99.931741 Neighbor list builds = 0 Dangerous builds = 0 1172 -4996.56348419637 eV 2.30991861150114 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11