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 = 3.61473 3.61473 3.61473 Created orthogonal box = (0 -65.0687 0) to (46.008 65.0687 5.112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.248 6.02455 5.112 Created 1299 atoms create_atoms CPU = 0.000642061 secs 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.248 6.02455 5.112 Created 1299 atoms create_atoms CPU = 0.000560999 secs 1299 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 30 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2580 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9022.2161 0 -9022.2161 7162.7664 125 0 -9075.0257 0 -9075.0257 -2994.081 Loop time of 2.88161 on 1 procs for 125 steps with 2580 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9022.21611316 -9075.01723449 -9075.02571162 Force two-norm initial, final = 58.7553 0.288012 Force max component initial, final = 14.0874 0.0547529 Final line search alpha, max atom move = 1 0.0547529 Iterations, force evaluations = 125 233 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8126 | 2.8126 | 2.8126 | 0.0 | 97.60 Neigh | 0.032553 | 0.032553 | 0.032553 | 0.0 | 1.13 Comm | 0.022793 | 0.022793 | 0.022793 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.47 Nlocal: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15571 ave 15571 max 15571 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: 578476 ave 578476 max 578476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578476 Ave neighs/atom = 224.216 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 : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -9075.0257 0 -9075.0257 -2994.081 30607.373 127 0 -9075.0685 0 -9075.0685 -2294.7353 30591.855 Loop time of 0.0536349 on 1 procs for 2 steps with 2580 atoms 111.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9075.02571162 -9075.06121787 -9075.06847001 Force two-norm initial, final = 51.0545 7.25587 Force max component initial, final = 49.6451 6.17447 Final line search alpha, max atom move = 5.28883e-05 0.000326557 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052206 | 0.052206 | 0.052206 | 0.0 | 97.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037313 | 0.00037313 | 0.00037313 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001056 | | | 1.97 Nlocal: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15573 ave 15573 max 15573 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: 578840 ave 578840 max 578840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578840 Ave neighs/atom = 224.357 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9075.0685 0 -9075.0685 -2294.7353 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2580 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: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15573 ave 15573 max 15573 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: 578880 ave 578880 max 578880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578880 Ave neighs/atom = 224.372 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) = 10.36 | 10.36 | 10.36 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 -9075.0685 -9075.0685 46.049265 130.13744 5.1048248 -2294.7353 -2294.7353 -199.17335 -6362.1128 -322.9198 2.3740673 1392.8123 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2580 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: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15573 ave 15573 max 15573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289440 ave 289440 max 289440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 578880 ave 578880 max 578880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578880 Ave neighs/atom = 224.372 Neighbor list builds = 0 Dangerous builds = 0 2580 -9075.06847001063 eV 2.37406725600401 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03