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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) create_atoms CPU = 0.002 seconds 1690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 74 atoms, new total = 3306 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.675 | 5.675 | 5.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13938.416 0 -13938.416 -9404.0593 209 0 -14001.197 0 -14001.197 -23086.438 Loop time of 90.0691 on 1 procs for 209 steps with 3306 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 = -13938.4155964879 -14001.184077125 -14001.1971200968 Force two-norm initial, final = 9.8035569 0.32407372 Force max component initial, final = 1.0402176 0.036598273 Final line search alpha, max atom move = 0.88194108 0.032277520 Iterations, force evaluations = 209 401 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 89.757 | 89.757 | 89.757 | 0.0 | 99.65 Neigh | 0.12912 | 0.12912 | 0.12912 | 0.0 | 0.14 Comm | 0.070169 | 0.070169 | 0.070169 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1128 | | | 0.13 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7674.00 ave 7674 max 7674 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: 248600.0 ave 248600 max 248600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248600 Ave neighs/atom = 75.196612 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 209 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.672 | 5.672 | 5.672 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -14001.197 0 -14001.197 -23086.438 39336.391 229 0 -14010.59 0 -14010.59 -1616.4646 38790.391 Loop time of 3.58992 on 1 procs for 20 steps with 3306 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14001.1971200968 -14010.5903909514 -14010.5904117311 Force two-norm initial, final = 1059.9198 1.2574019 Force max component initial, final = 1042.2011 0.64871409 Final line search alpha, max atom move = 0.0011434811 0.00074179231 Iterations, force evaluations = 20 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5279 | 3.5279 | 3.5279 | 0.0 | 98.27 Neigh | 0.042945 | 0.042945 | 0.042945 | 0.0 | 1.20 Comm | 0.0026905 | 0.0026905 | 0.0026905 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0164 | | | 0.46 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7552.00 ave 7552 max 7552 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: 249188.0 ave 249188 max 249188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249188 Ave neighs/atom = 75.374471 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.810 | 5.810 | 5.810 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14010.59 0 -14010.59 -1616.4646 Loop time of 4.21e-06 on 1 procs for 0 steps with 3306 atoms 166.3% 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 | | 4.21e-06 | | |100.00 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7546.00 ave 7546 max 7546 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: 248908.0 ave 248908 max 248908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248908 Ave neighs/atom = 75.289776 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 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.810 | 5.810 | 5.810 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 -14010.59 -14010.59 51.261378 85.301544 8.8710903 -1616.4646 -1616.4646 26.29626 -4896.1856 20.49555 2.374608 6676.7229 Loop time of 4.459e-06 on 1 procs for 0 steps with 3306 atoms 224.3% 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 | | 4.459e-06 | | |100.00 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7546.00 ave 7546 max 7546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124454.0 ave 124454 max 124454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248908.0 ave 248908 max 248908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248908 Ave neighs/atom = 75.289776 Neighbor list builds = 0 Dangerous builds = 0 3306 -14010.5904117311 eV 2.37460795149491 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:34