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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -43.5203 0) to (14.5056 43.5203 3.51812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.26635 4.26635 3.51812 Created 206 atoms create_atoms CPU = 0.000171185 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.26635 4.26635 3.51812 Created 206 atoms create_atoms CPU = 4.60148e-05 secs 206 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 1 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 8 atoms, new total = 404 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 1 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) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1749.3097 0 -1749.3097 16927.406 40 0 -1763.1068 0 -1763.1068 -7506.2591 Loop time of 0.154498 on 1 procs for 40 steps with 404 atoms 103.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1749.30968268 -1763.10562849 -1763.10684488 Force two-norm initial, final = 61.2394 0.0938054 Force max component initial, final = 20.3349 0.0137994 Final line search alpha, max atom move = 1 0.0137994 Iterations, force evaluations = 40 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14867 | 0.14867 | 0.14867 | 0.0 | 96.23 Neigh | 0.0022068 | 0.0022068 | 0.0022068 | 0.0 | 1.43 Comm | 0.0024786 | 0.0024786 | 0.0024786 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001143 | | | 0.74 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5112 ave 5112 max 5112 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: 79916 ave 79916 max 79916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79916 Ave neighs/atom = 197.812 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.508 | 4.508 | 4.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1763.1068 0 -1763.1068 -7506.2591 4441.8885 43 0 -1763.1472 0 -1763.1472 -802.54303 4424.4361 Loop time of 0.0108569 on 1 procs for 3 steps with 404 atoms 92.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1763.10684488 -1763.14710269 -1763.14721434 Force two-norm initial, final = 29.1917 0.392686 Force max component initial, final = 21.0723 0.310682 Final line search alpha, max atom move = 0.00142349 0.000442254 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010286 | 0.010286 | 0.010286 | 0.0 | 94.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015068 | 0.00015068 | 0.00015068 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004201 | | | 3.87 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5145 ave 5145 max 5145 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: 80044 ave 80044 max 80044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80044 Ave neighs/atom = 198.129 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 1 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1763.1472 0 -1763.1472 -802.54303 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 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 | | 1.192e-06 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5145 ave 5145 max 5145 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: 80092 ave 80092 max 80092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80092 Ave neighs/atom = 198.248 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) = 4.646 | 4.646 | 4.646 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 -1763.1472 -1763.1472 14.480729 87.040547 3.5103133 -802.54303 -802.54303 112.31149 -2597.1351 77.1945 2.2458378 181.51463 Loop time of 2.14577e-06 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5145 ave 5145 max 5145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40046 ave 40046 max 40046 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80092 ave 80092 max 80092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80092 Ave neighs/atom = 198.248 Neighbor list builds = 0 Dangerous builds = 0 404 -1763.14721433619 eV 2.2458377958319 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00