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 = 4.12887 4.12887 4.12887 Created orthogonal box = (0 -43.3081 0) to (53.0363 43.3081 10.1136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.75008 6.29876 6.74242 Created 1322 atoms create_atoms CPU = 0.00067687 secs 1322 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.75008 6.29876 6.74242 Created 1322 atoms create_atoms CPU = 0.000605106 secs 1322 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 19 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 2604 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.468 | 6.468 | 6.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9599.8689 0 -9599.8689 -7267.0764 50 0 -9641.1166 0 -9641.1166 -10648.222 Loop time of 1.49503 on 1 procs for 50 steps with 2604 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 = -9599.86894185 -9641.10757819 -9641.11656653 Force two-norm initial, final = 32.2323 0.220113 Force max component initial, final = 4.98247 0.0311575 Final line search alpha, max atom move = 1 0.0311575 Iterations, force evaluations = 50 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4567 | 1.4567 | 1.4567 | 0.0 | 97.43 Neigh | 0.028209 | 0.028209 | 0.028209 | 0.0 | 1.89 Comm | 0.005022 | 0.005022 | 0.005022 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005145 | | | 0.34 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9162 ave 9162 max 9162 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: 462460 ave 462460 max 462460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462460 Ave neighs/atom = 177.596 Neighbor list builds = 2 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.469 | 6.469 | 6.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -9641.1166 0 -9641.1166 -10648.222 46460.024 56 0 -9642.3361 0 -9642.3361 -1918.3441 46057.112 Loop time of 0.177238 on 1 procs for 6 steps with 2604 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9641.11656653 -9642.32925358 -9642.33614887 Force two-norm initial, final = 387.815 0.331674 Force max component initial, final = 291.307 0.109691 Final line search alpha, max atom move = 8.36658e-05 9.17741e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1746 | 0.1746 | 0.1746 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049043 | 0.00049043 | 0.00049043 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00215 | | | 1.21 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9153 ave 9153 max 9153 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: 461208 ave 461208 max 461208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461208 Ave neighs/atom = 177.115 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.61 | 6.61 | 6.61 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9642.3361 0 -9642.3361 -1918.3441 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2604 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 | | 9.537e-07 | | |100.00 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9445 ave 9445 max 9445 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: 475582 ave 475582 max 475582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475582 Ave neighs/atom = 182.635 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) = 6.61 | 6.61 | 6.61 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 -9642.3361 -9642.3361 52.871748 86.616196 10.057127 -1918.3441 -1918.3441 2.99479 -5761.8217 3.7944857 2.6259688 2208.4247 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2604 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 | | 2.146e-06 | | |100.00 Nlocal: 2604 ave 2604 max 2604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9445 ave 9445 max 9445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237791 ave 237791 max 237791 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 475582 ave 475582 max 475582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475582 Ave neighs/atom = 182.635 Neighbor list builds = 0 Dangerous builds = 0 2604 -9642.33614887191 eV 2.62596881970138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02