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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -39.840000 0.0000000) to (6.0992294 39.840000 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0992294 4.9800000 5.7504086 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (6.0992294 39.840000 8.6256130) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0992294 4.9800000 5.7504086 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (6.0992294 39.840000 8.6256130) create_atoms CPU = 0.000 seconds 198 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 = 3 27 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 6 atoms, new total = 384 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_912636107108_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 = 3 27 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) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1708.8 0 -1708.8 0.014455217 1 0 -1708.8 0 -1708.8 0.014455217 Loop time of 0.0429284 on 1 procs for 1 steps with 384 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 = -1708.80000001421 -1708.80000001421 -1708.80000001421 Force two-norm initial, final = 1.4878097e-07 4.7025018e-08 Force max component initial, final = 3.8653812e-08 1.2398031e-08 Final line search alpha, max atom move = 1.0000000 1.2398031e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042713 | 0.042713 | 0.042713 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.3999e-05 | 7.3999e-05 | 7.3999e-05 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001417 | | | 0.33 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2464.00 ave 2464 max 2464 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: 29952.0 ave 29952 max 29952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29952 Ave neighs/atom = 78.000000 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 = 3 27 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1708.8 0 -1708.8 0.014455217 4191.9323 2 0 -1708.8 0 -1708.8 -3.5886246e-06 4191.9323 Loop time of 0.0398079 on 1 procs for 1 steps with 384 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1708.80000001421 -1708.80000001421 -1708.80000001418 Force two-norm initial, final = 6.5508628e-05 2.5829208e-07 Force max component initial, final = 3.8023678e-05 2.1627129e-07 Final line search alpha, max atom move = 1.0000000 2.1627129e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039415 | 0.039415 | 0.039415 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.7961e-05 | 6.7961e-05 | 6.7961e-05 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003252 | | | 0.82 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2464.00 ave 2464 max 2464 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: 29952.0 ave 29952 max 29952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29952 Ave neighs/atom = 78.000000 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 = 3 27 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1708.8 0 -1708.8 -3.5886242e-06 Loop time of 1.996e-06 on 1 procs for 0 steps with 384 atoms 150.3% 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 | | 1.996e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2464.00 ave 2464 max 2464 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: 29952.0 ave 29952 max 29952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29952 Ave neighs/atom = 78.000000 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 = 3 27 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) = 4.580 | 4.580 | 4.580 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 -1708.8 -1708.8 6.0992294 79.68 8.625613 -3.5886242e-06 -3.5886242e-06 3.768389e-05 -8.2659917e-05 3.4210154e-05 2.49 2.6494987e-16 Loop time of 1.82e-06 on 1 procs for 0 steps with 384 atoms 164.8% 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 | | 1.82e-06 | | |100.00 Nlocal: 384.000 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2464.00 ave 2464 max 2464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14976.0 ave 14976 max 14976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29952.0 ave 29952 max 29952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29952 Ave neighs/atom = 78.000000 Neighbor list builds = 0 Dangerous builds = 0 384 -1708.80000001418 eV 2.48999999154132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00