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 = 3.6583 3.6583 3.6583 Created orthogonal box = (0 -43.9032 0) to (15.5208 43.9032 5.17361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.17361 6.09716 5.17361 Created 292 atoms create_atoms CPU = 0.000305891 secs 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.17361 6.09716 5.17361 Created 292 atoms create_atoms CPU = 0.000183105 secs 292 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 ghost atom cutoff = 8 binsize = 4, bins = 4 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 574 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 ghost atom cutoff = 8 binsize = 4, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.93 | 4.93 | 4.93 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2154.376 0 -2154.376 137610.78 429 0 -2317.6928 0 -2317.6928 -61412.177 Loop time of 2.10052 on 1 procs for 429 steps with 574 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 = -2154.37599948 -2317.69064805 -2317.69282393 Force two-norm initial, final = 272.036 0.15524 Force max component initial, final = 60.1907 0.0237118 Final line search alpha, max atom move = 1 0.0237118 Iterations, force evaluations = 429 815 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0325 | 2.0325 | 2.0325 | 0.0 | 96.76 Neigh | 0.024034 | 0.024034 | 0.024034 | 0.0 | 1.14 Comm | 0.028957 | 0.028957 | 0.028957 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01503 | | | 0.72 Nlocal: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5061 ave 5061 max 5061 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: 97084 ave 97084 max 97084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97084 Ave neighs/atom = 169.136 Neighbor list builds = 8 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 : 429 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.93 | 4.93 | 4.93 Mbytes Step Temp E_pair E_mol TotEng Press Volume 429 0 -2317.6928 0 -2317.6928 -61412.177 7050.7503 469 0 -2326.6035 0 -2326.6035 -8729.3537 6791.3388 Loop time of 0.115871 on 1 procs for 40 steps with 574 atoms 94.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2317.69282393 -2326.60246364 -2326.60352821 Force two-norm initial, final = 443.567 5.76663 Force max component initial, final = 423.98 4.9236 Final line search alpha, max atom move = 0.0027885 0.0137294 Iterations, force evaluations = 40 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10971 | 0.10971 | 0.10971 | 0.0 | 94.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013857 | 0.0013857 | 0.0013857 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004771 | | | 4.12 Nlocal: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5052 ave 5052 max 5052 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: 97016 ave 97016 max 97016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97016 Ave neighs/atom = 169.017 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 ghost atom cutoff = 8 binsize = 4, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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/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) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2326.6035 0 -2326.6035 -8729.3537 Loop time of 9.53674e-07 on 1 procs for 0 steps with 574 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: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5200 ave 5200 max 5200 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: 99696 ave 99696 max 99696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99696 Ave neighs/atom = 173.686 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) = 5.069 | 5.069 | 5.069 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 -2326.6035 -2326.6035 15.55074 87.806429 4.9736822 -8729.3537 -8729.3537 617.07706 -27921.8 1116.6615 2.2777167 1332.7546 Loop time of 1.90735e-06 on 1 procs for 0 steps with 574 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: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5200 ave 5200 max 5200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49848 ave 49848 max 49848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99696 ave 99696 max 99696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99696 Ave neighs/atom = 173.686 Neighbor list builds = 0 Dangerous builds = 0 574 -2326.60352820991 eV 2.27771672314347 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02