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 = 3.61494 3.61494 3.61494 Created orthogonal box = (0 -36.8689 0) to (31.9263 36.8689 6.26126) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.73036 5.67158 6.26126 Created 628 atoms create_atoms CPU = 0.000277996 secs 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.73036 5.67158 6.26126 Created 629 atoms create_atoms CPU = 0.000199795 secs 629 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 8 18 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 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1233 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 5.476 | 5.476 | 5.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4297.5473 0 -4297.5473 9398.2229 88 0 -4345.3502 0 -4345.3502 -1951.2077 Loop time of 0.907917 on 1 procs for 88 steps with 1233 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4297.54729742 -4345.34673415 -4345.35023258 Force two-norm initial, final = 53.9088 0.19018 Force max component initial, final = 10.2168 0.0553064 Final line search alpha, max atom move = 1 0.0553064 Iterations, force evaluations = 88 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87485 | 0.87485 | 0.87485 | 0.0 | 96.36 Neigh | 0.020334 | 0.020334 | 0.020334 | 0.0 | 2.24 Comm | 0.0079234 | 0.0079234 | 0.0079234 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004805 | | | 0.53 Nlocal: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7477 ave 7477 max 7477 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: 245676 ave 245676 max 245676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245676 Ave neighs/atom = 199.251 Neighbor list builds = 3 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.478 | 5.478 | 5.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4345.3502 0 -4345.3502 -1951.2077 14740.089 91 0 -4345.3752 0 -4345.3752 -576.32993 14725.636 Loop time of 0.0314469 on 1 procs for 3 steps with 1233 atoms 95.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4345.35023258 -4345.37514225 -4345.37516403 Force two-norm initial, final = 30.3887 0.210406 Force max component initial, final = 30.3837 0.0574822 Final line search alpha, max atom move = 0.00117117 6.73216e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030483 | 0.030483 | 0.030483 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023508 | 0.00023508 | 0.00023508 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007291 | | | 2.32 Nlocal: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7485 ave 7485 max 7485 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: 245690 ave 245690 max 245690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245690 Ave neighs/atom = 199.262 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 5.617 | 5.617 | 5.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4345.3752 0 -4345.3752 -576.32993 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1233 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: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7549 ave 7549 max 7549 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: 245784 ave 245784 max 245784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245784 Ave neighs/atom = 199.338 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) = 5.617 | 5.617 | 5.617 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 -4345.3752 -4345.3752 31.947491 73.737809 6.2509651 -576.32993 -576.32993 -3.684488 -1721.8415 -3.4638155 2.3079565 940.37292 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1233 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: 1233 ave 1233 max 1233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7549 ave 7549 max 7549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122892 ave 122892 max 122892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245784 ave 245784 max 245784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245784 Ave neighs/atom = 199.338 Neighbor list builds = 0 Dangerous builds = 0 1233 -4345.37516403432 eV 2.30795645200419 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01