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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -53.574728 0.0000000) to (43.740626 53.574728 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3926799 5.1369555 5.9114352 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.574728 0.0000000) to (43.740626 53.574728 8.8671528) create_atoms CPU = 0.007 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3926799 5.1369555 5.9114352 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.574728 0.0000000) to (43.740626 53.574728 8.8671528) create_atoms CPU = 0.007 seconds 1757 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 = 15 36 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 45 atoms, new total = 3469 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_313717476091_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 = 15 36 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) = 5.697 | 5.697 | 5.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12170.652 0 -12170.652 -14.200918 18 0 -12216.887 0 -12216.887 -3179.2177 Loop time of 3.69955 on 1 procs for 18 steps with 3469 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12170.6517322419 -12216.8771197744 -12216.8868896114 Force two-norm initial, final = 42.196989 0.83234459 Force max component initial, final = 6.3418009 0.15229809 Final line search alpha, max atom move = 1.0000000 0.15229809 Iterations, force evaluations = 18 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6828 | 3.6828 | 3.6828 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0062506 | 0.0062506 | 0.0062506 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01048 | | | 0.28 Nlocal: 3469.00 ave 3469 max 3469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 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: 267638.0 ave 267638 max 267638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267638 Ave neighs/atom = 77.151340 Neighbor list builds = 0 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 = 15 36 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.697 | 5.697 | 5.697 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -12216.887 0 -12216.887 -3179.2177 41558.432 20 0 -12217.021 0 -12217.021 327.45245 41451.358 Loop time of 0.450321 on 1 procs for 2 steps with 3469 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 = -12216.8868896114 -12217.012433849 -12217.0205086871 Force two-norm initial, final = 146.30507 1.9757365 Force max component initial, final = 106.28076 1.2572567 Final line search alpha, max atom move = 3.8442513e-05 4.8332105e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44649 | 0.44649 | 0.44649 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074323 | 0.00074323 | 0.00074323 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003092 | | | 0.69 Nlocal: 3469.00 ave 3469 max 3469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 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: 267616.0 ave 267616 max 267616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267616 Ave neighs/atom = 77.144999 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 = 15 36 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) = 5.835 | 5.835 | 5.835 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12217.021 0 -12217.021 327.45245 Loop time of 6.204e-06 on 1 procs for 0 steps with 3469 atoms 193.4% 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 | | 6.204e-06 | | |100.00 Nlocal: 3469.00 ave 3469 max 3469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 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: 267624.0 ave 267624 max 267624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267624 Ave neighs/atom = 77.147305 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 = 15 36 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) = 5.835 | 5.835 | 5.835 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 -12217.021 -12217.021 43.685111 107.14946 8.8555461 327.45245 327.45245 -48.533766 984.22076 46.670357 2.2999081 1996.7503 Loop time of 6.475e-06 on 1 procs for 0 steps with 3469 atoms 293.4% 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 | | 6.475e-06 | | |100.00 Nlocal: 3469.00 ave 3469 max 3469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133812.0 ave 133812 max 133812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267624.0 ave 267624 max 267624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267624 Ave neighs/atom = 77.147305 Neighbor list builds = 0 Dangerous builds = 0 3469 -12217.0205086871 eV 2.29990811396494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05