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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -44.568832 0.0000000) to (5.1463654 44.568832 6.3029846) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1463654 5.9425109 6.3029846 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.568832 0.0000000) to (5.1463654 44.568832 6.3029846) create_atoms CPU = 0.002 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1463654 5.9425109 6.3029846 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.568832 0.0000000) to (5.1463654 44.568832 6.3029846) create_atoms CPU = 0.002 seconds 122 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_748636486270_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -821.4526 0 -821.4526 -0.043715972 1 0 -821.4526 0 -821.4526 -0.043715972 Loop time of 0.0164763 on 1 procs for 1 steps with 240 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -821.452599111414 -821.452599111414 -821.452599111413 Force two-norm initial, final = 8.0510826e-08 2.8430265e-08 Force max component initial, final = 2.4758325e-08 9.2313459e-09 Final line search alpha, max atom move = 1.0000000 9.2313459e-09 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015963 | 0.015963 | 0.015963 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025013 | 0.00025013 | 0.00025013 | 0.0 | 1.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002628 | | | 1.59 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 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: 42240.0 ave 42240 max 42240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42240 Ave neighs/atom = 176.00000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.512 | 4.512 | 4.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -821.4526 0 -821.4526 -0.043715972 2891.3996 2 0 -821.4526 0 -821.4526 -1.6281296e-05 2891.3995 Loop time of 0.0169844 on 1 procs for 1 steps with 240 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 = -821.452599111412 -821.452599111412 -821.452599111467 Force two-norm initial, final = 0.00013664661 1.2592605e-07 Force max component initial, final = 7.9027783e-05 1.2036869e-07 Final line search alpha, max atom move = 1.0000000 1.2036869e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01612 | 0.01612 | 0.01612 | 0.0 | 94.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002311 | 0.0002311 | 0.0002311 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006333 | | | 3.73 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 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: 42240.0 ave 42240 max 42240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42240 Ave neighs/atom = 176.00000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -821.4526 0 -821.4526 -1.6281296e-05 Loop time of 5.953e-06 on 1 procs for 0 steps with 240 atoms 117.6% 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 | | 5.953e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 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: 42240.0 ave 42240 max 42240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42240 Ave neighs/atom = 176.00000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 2 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.650 | 4.650 | 4.650 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 -821.4526 -821.4526 5.1463654 89.137663 6.3029846 -1.6281296e-05 -1.6281296e-05 6.3650808e-06 -6.6698454e-05 1.1489484e-05 2.5731827 3.319341e-16 Loop time of 6.384e-06 on 1 procs for 0 steps with 240 atoms 156.6% 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 | | 6.384e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21120.0 ave 21120 max 21120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42240.0 ave 42240 max 42240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42240 Ave neighs/atom = 176.00000 Neighbor list builds = 0 Dangerous builds = 0 240 -821.452599111467 eV 2.57318268051192 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00