LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -45.0841 0) to (9.01601 45.0841 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.40961 5.40961 4.03208 Created 102 atoms create_atoms CPU = 0.000276089 secs 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.40961 5.40961 4.03208 Created 102 atoms create_atoms CPU = 0.000133991 secs 102 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1146) 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 3 24 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 198 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.415 | 4.415 | 4.415 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -657.16462 0 -657.16462 6614.4254 93 0 -663.18238 0 -663.18238 -989.23237 Loop time of 0.171347 on 1 procs for 93 steps with 198 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 = -657.16461908 -663.181881277 -663.182378281 Force two-norm initial, final = 15.1179 0.0509541 Force max component initial, final = 4.6341 0.0102425 Final line search alpha, max atom move = 1 0.0102425 Iterations, force evaluations = 93 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16772 | 0.16772 | 0.16772 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026526 | 0.0026526 | 0.0026526 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009761 | | | 0.57 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2587 ave 2587 max 2587 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: 25920 ave 25920 max 25920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25920 Ave neighs/atom = 130.909 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.415 | 4.415 | 4.415 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -663.18238 0 -663.18238 -989.23237 3277.9109 96 0 -663.18958 0 -663.18958 1219.9806 3268.8967 Loop time of 0.00585103 on 1 procs for 3 steps with 198 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 = -663.182378281 -663.189555413 -663.189576984 Force two-norm initial, final = 7.26726 0.0664128 Force max component initial, final = 5.55043 0.0184662 Final line search alpha, max atom move = 0.00636518 0.000117541 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0055294 | 0.0055294 | 0.0055294 | 0.0 | 94.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.7976e-05 | 8.7976e-05 | 8.7976e-05 | 0.0 | 1.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002337 | | | 3.99 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2567 ave 2567 max 2567 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: 24264 ave 24264 max 24264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24264 Ave neighs/atom = 122.545 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -663.18958 0 -663.18958 1219.9806 Loop time of 9.53674e-07 on 1 procs for 0 steps with 198 atoms 209.7% 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: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2571 ave 2571 max 2571 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: 24532 ave 24532 max 24532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24532 Ave neighs/atom = 123.899 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) = 4.552 | 4.552 | 4.552 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 -663.18958 -663.18958 9.0010471 90.168175 4.0276794 1219.9806 1219.9806 3.7065941 3665.2761 -9.0409096 2.5983458 195.62286 Loop time of 9.53674e-07 on 1 procs for 0 steps with 198 atoms 104.9% 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: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2571 ave 2571 max 2571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12266 ave 12266 max 12266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24532 ave 24532 max 24532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24532 Ave neighs/atom = 123.899 Neighbor list builds = 0 Dangerous builds = 0 198 -663.18957698366 eV 2.59834581033019 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00