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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -51.514537 0.0000000) to (36.424053 51.514537 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4364259 4.9973737 4.4499063 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -51.514537 0.0000000) to (36.424053 51.514537 4.4499063) create_atoms CPU = 0.005 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4364259 4.9973737 4.4499063 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -51.514537 0.0000000) to (36.424053 51.514537 4.4499063) create_atoms CPU = 0.004 seconds 538 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 36 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1068 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_805823015127_000#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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7207.5573 0 -7207.5573 8225.9444 35 0 -7248.6142 0 -7248.6142 -3646.787 Loop time of 3.55729 on 1 procs for 35 steps with 1068 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 = -7207.55733166202 -7248.60921688259 -7248.61415172835 Force two-norm initial, final = 33.612917 0.23533628 Force max component initial, final = 5.5813073 0.021303159 Final line search alpha, max atom move = 1.0000000 0.021303159 Iterations, force evaluations = 35 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5418 | 3.5418 | 3.5418 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0072494 | 0.0072494 | 0.0072494 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008261 | | | 0.23 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204.00 ave 5204 max 5204 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: 61412.0 ave 61412 max 61412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61412 Ave neighs/atom = 57.501873 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -7248.6142 0 -7248.6142 -3646.787 16699.326 37 0 -7248.6538 0 -7248.6538 156.39286 16675.204 Loop time of 0.298024 on 1 procs for 2 steps with 1068 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 = -7248.61415172836 -7248.651386127 -7248.65383739453 Force two-norm initial, final = 67.128563 0.24162478 Force max component initial, final = 58.179558 0.022775395 Final line search alpha, max atom move = 0.00011828768 2.6940487e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29554 | 0.29554 | 0.29554 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053626 | 0.00053626 | 0.00053626 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001949 | | | 0.65 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5172.00 ave 5172 max 5172 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: 61512.0 ave 61512 max 61512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61512 Ave neighs/atom = 57.595506 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.731 | 4.731 | 4.731 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7248.6538 0 -7248.6538 156.39286 Loop time of 7.187e-06 on 1 procs for 0 steps with 1068 atoms 180.9% 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 | | 7.187e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5172.00 ave 5172 max 5172 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: 61512.0 ave 61512 max 61512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61512 Ave neighs/atom = 57.595506 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.731 | 4.731 | 4.731 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 -7248.6538 -7248.6538 36.416991 103.02907 4.4443402 156.39286 156.39286 0.15482013 468.17861 0.84514059 2.3685686 553.72722 Loop time of 6.876e-06 on 1 procs for 0 steps with 1068 atoms 290.9% 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 | | 6.876e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5172.00 ave 5172 max 5172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30756.0 ave 30756 max 30756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61512.0 ave 61512 max 61512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61512 Ave neighs/atom = 57.595506 Neighbor list builds = 0 Dangerous builds = 0 1068 -7248.65383739453 eV 2.36856862273643 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04