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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -65.470437 0.0000000) to (23.147295 65.470437 5.1123823) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2102499 5.5889398 5.1123823 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.470437 0.0000000) to (23.147295 65.470437 5.1123823) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2102499 5.5889398 5.1123823 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.470437 0.0000000) to (23.147295 65.470437 5.1123823) create_atoms CPU = 0.002 seconds 658 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.505 | 5.505 | 5.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4526.689 0 -4526.689 9027.6244 182 0 -4637.6331 0 -4637.6331 2204.1648 Loop time of 3.16634 on 1 procs for 182 steps with 1312 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4526.68897849917 -4637.62936935406 -4637.63310357807 Force two-norm initial, final = 50.767095 0.17546469 Force max component initial, final = 9.4307998 0.025425342 Final line search alpha, max atom move = 1.0000000 0.025425342 Iterations, force evaluations = 182 320 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0281 | 3.0281 | 3.0281 | 0.0 | 95.64 Neigh | 0.090052 | 0.090052 | 0.090052 | 0.0 | 2.84 Comm | 0.026465 | 0.026465 | 0.026465 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02169 | | | 0.69 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 219440.0 ave 219440 max 219440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219440 Ave neighs/atom = 167.25610 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 182 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.505 | 5.505 | 5.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 182 0 -4637.6331 0 -4637.6331 2204.1648 15495.258 185 0 -4637.6722 0 -4637.6722 -52.284278 15520.449 Loop time of 0.0552215 on 1 procs for 3 steps with 1312 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 = -4637.63310357808 -4637.67205910327 -4637.67222230989 Force two-norm initial, final = 44.685054 1.4942493 Force max component initial, final = 38.767986 1.1161101 Final line search alpha, max atom move = 0.00034200177 0.00038171163 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053284 | 0.053284 | 0.053284 | 0.0 | 96.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037092 | 0.00037092 | 0.00037092 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001567 | | | 2.84 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 221344.0 ave 221344 max 221344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 221344 Ave neighs/atom = 168.70732 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.643 | 5.643 | 5.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4637.6722 0 -4637.6722 -52.284278 Loop time of 1.72e-06 on 1 procs for 0 steps with 1312 atoms 174.4% 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 | | 1.72e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 219620.0 ave 219620 max 219620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219620 Ave neighs/atom = 167.39329 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.643 | 5.643 | 5.643 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 -4637.6722 -4637.6722 23.187006 131.03183 5.1083752 -52.284278 -52.284278 -115.41375 47.521356 -88.960442 2.3847419 552.65242 Loop time of 1.95e-06 on 1 procs for 0 steps with 1312 atoms 153.8% 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 | | 1.95e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109810.0 ave 109810 max 109810 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219620.0 ave 219620 max 219620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219620 Ave neighs/atom = 167.39329 Neighbor list builds = 0 Dangerous builds = 0 1312 -4637.67222230989 eV 2.38474193342725 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03