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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.690605 0.0000000) to (6.1787847 43.690605 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1787847 5.8254141 5.0449566 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.690605 0.0000000) to (6.1787847 43.690605 5.0449566) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1787847 5.8254141 5.0449566 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.690605 0.0000000) to (6.1787847 43.690605 5.0449566) create_atoms CPU = 0.000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 32 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 242 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -962.77139 0 -962.77139 84069.277 167 0 -1020.6818 0 -1020.6818 67797.198 Loop time of 2.78444 on 1 procs for 167 steps with 242 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 = -962.771389658888 -1020.6810143447 -1020.68183277771 Force two-norm initial, final = 102.27650 0.12228067 Force max component initial, final = 27.951110 0.019821132 Final line search alpha, max atom move = 1.0000000 0.019821132 Iterations, force evaluations = 167 325 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7702 | 2.7702 | 2.7702 | 0.0 | 99.49 Neigh | 0.0011845 | 0.0011845 | 0.0011845 | 0.0 | 0.04 Comm | 0.0072285 | 0.0072285 | 0.0072285 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005813 | | | 0.21 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2144.00 ave 2144 max 2144 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: 14740.0 ave 14740 max 14740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14740 Ave neighs/atom = 60.909091 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 167 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 167 0 -1020.6818 0 -1020.6818 67797.198 2723.8209 192 0 -1022.0121 0 -1022.0121 647.24558 2799.8447 Loop time of 0.229825 on 1 procs for 25 steps with 242 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1020.68183277771 -1022.0115814322 -1022.0120942316 Force two-norm initial, final = 200.44225 2.5736081 Force max component initial, final = 125.87502 1.3360468 Final line search alpha, max atom move = 0.00059407100 0.00079370668 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22407 | 0.22407 | 0.22407 | 0.0 | 97.49 Neigh | 0.0023708 | 0.0023708 | 0.0023708 | 0.0 | 1.03 Comm | 0.00065449 | 0.00065449 | 0.00065449 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002732 | | | 1.19 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2146.00 ave 2146 max 2146 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: 13696.0 ave 13696 max 13696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13696 Ave neighs/atom = 56.595041 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1022.0121 0 -1022.0121 647.24558 Loop time of 2.136e-06 on 1 procs for 0 steps with 242 atoms 140.4% 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 | | 2.136e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2146.00 ave 2146 max 2146 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: 13708.0 ave 13708 max 13708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13708 Ave neighs/atom = 56.644628 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.575 | 4.575 | 4.575 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 -1022.0121 -1022.0121 6.2374251 89.476006 5.0167447 647.24558 647.24558 619.60546 561.87036 760.26092 2.4390085 270.96995 Loop time of 2.025e-06 on 1 procs for 0 steps with 242 atoms 197.5% 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 | | 2.025e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2146.00 ave 2146 max 2146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6854.00 ave 6854 max 6854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13708.0 ave 13708 max 13708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13708 Ave neighs/atom = 56.644628 Neighbor list builds = 0 Dangerous builds = 0 242 -1022.0120942316 eV 2.43900845159583 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03