LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.58787 3.58787 3.58787 Created orthogonal box = (0 -38.3116 0) to (27.0878 38.3116 5.07402) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.17793 6.04863 5.07402 Created 458 atoms create_atoms CPU = 0.000403881 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.17793 6.04863 5.07402 Created 458 atoms create_atoms CPU = 0.000274897 secs 458 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 7 19 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 8.23106 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3136.8055 0 -3136.8055 14025.604 62 0 -3172.11 0 -3172.11 -5897.9025 Loop time of 1.14321 on 1 procs for 62 steps with 904 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3136.80552853 -3172.10713757 -3172.10995824 Force two-norm initial, final = 51.4807 0.167354 Force max component initial, final = 15.3356 0.0243985 Final line search alpha, max atom move = 1 0.0243985 Iterations, force evaluations = 62 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1326 | 1.1326 | 1.1326 | 0.0 | 99.07 Neigh | 0.0034401 | 0.0034401 | 0.0034401 | 0.0 | 0.30 Comm | 0.0045934 | 0.0045934 | 0.0045934 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002582 | | | 0.23 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6545 ave 6545 max 6545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179636 ave 179636 max 179636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179636 Ave neighs/atom = 198.712 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3172.11 0 -3172.11 -5897.9025 10531.402 65 0 -3172.138 0 -3172.138 -3708.6078 10514.976 Loop time of 0.0410709 on 1 procs for 3 steps with 904 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3172.10995824 -3172.13724798 -3172.13796909 Force two-norm initial, final = 28.847 0.467428 Force max component initial, final = 28.3755 0.428277 Final line search alpha, max atom move = 0.000187345 8.02353e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040484 | 0.040484 | 0.040484 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015807 | 0.00015807 | 0.00015807 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004289 | | | 1.04 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6577 ave 6577 max 6577 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179876 ave 179876 max 179876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179876 Ave neighs/atom = 198.978 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3172.138 0 -3172.138 -3708.6078 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6559 ave 6559 max 6559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179944 ave 179944 max 179944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179944 Ave neighs/atom = 199.053 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.139 | 5.139 | 5.139 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 -3172.138 -3172.138 27.100223 76.623147 5.0637869 -3708.6078 -3708.6078 -6.4799676 -11054.218 -65.125323 2.365876 798.32518 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6559 ave 6559 max 6559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89972 ave 89972 max 89972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179944 ave 179944 max 179944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179944 Ave neighs/atom = 199.053 Neighbor list builds = 0 Dangerous builds = 0 904 -3172.13796909331 eV 2.36587597418654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01