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 -66.460810 0.0000000) to (33.230405 66.460810 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 679 atoms using lattice units in orthogonal box = (0.0000000 -66.460810 0.0000000) to (33.230405 66.460810 3.6043435) create_atoms CPU = 0.001 seconds 679 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -66.460810 0.0000000) to (33.230405 66.460810 3.6043435) create_atoms CPU = 0.001 seconds 681 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 = 12 45 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1360 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 = 12 45 2 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) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5663.6995 0 -5663.6995 23505.178 64 0 -5767.8351 0 -5767.8351 1450.4812 Loop time of 5.23336 on 1 procs for 64 steps with 1360 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 = -5663.69954914624 -5767.82966058932 -5767.83513228232 Force two-norm initial, final = 118.39450 0.21721398 Force max component initial, final = 33.272881 0.042213362 Final line search alpha, max atom move = 1.0000000 0.042213362 Iterations, force evaluations = 64 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1986 | 5.1986 | 5.1986 | 0.0 | 99.34 Neigh | 0.015766 | 0.015766 | 0.015766 | 0.0 | 0.30 Comm | 0.010087 | 0.010087 | 0.010087 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008901 | | | 0.17 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7723.00 ave 7723 max 7723 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: 105690.0 ave 105690 max 105690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105690 Ave neighs/atom = 77.713235 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 ghost atom cutoff = 6 binsize = 3, bins = 12 45 2 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -5767.8351 0 -5767.8351 1450.4812 15920.527 76 0 -5768.2283 0 -5768.2283 -309.8466 15936.801 Loop time of 0.658055 on 1 procs for 12 steps with 1360 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 = -5767.83513228232 -5768.22600635402 -5768.22833221005 Force two-norm initial, final = 61.067410 6.5389025 Force max component initial, final = 51.666654 4.6403225 Final line search alpha, max atom move = 7.4337915e-05 0.00034495190 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65274 | 0.65274 | 0.65274 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085621 | 0.00085621 | 0.00085621 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004457 | | | 0.68 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7733.00 ave 7733 max 7733 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: 105698.0 ave 105698 max 105698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105698 Ave neighs/atom = 77.719118 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 = 12 45 2 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) = 5.200 | 5.200 | 5.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5768.2283 0 -5768.2283 -309.8466 Loop time of 1.686e-06 on 1 procs for 0 steps with 1360 atoms 177.9% 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 | | 1.686e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7755.00 ave 7755 max 7755 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: 105728.0 ave 105728 max 105728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105728 Ave neighs/atom = 77.741176 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 = 12 45 2 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) = 5.200 | 5.200 | 5.200 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 -5768.2283 -5768.2283 33.01031 132.42068 3.6458241 -309.8466 -309.8466 -463.41635 -459.05001 -7.073462 2.2886509 152.47135 Loop time of 3.444e-06 on 1 procs for 0 steps with 1360 atoms 203.3% 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 | | 3.444e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7755.00 ave 7755 max 7755 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52864.0 ave 52864 max 52864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105728.0 ave 105728 max 105728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105728 Ave neighs/atom = 77.741176 Neighbor list builds = 0 Dangerous builds = 0 1360 -5768.22833221005 eV 2.28865089713994 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06