LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8553247 2.8553247 2.8553247 Created orthogonal box = (0.0000000 -49.455674 0.0000000) to (20.190194 49.455674 6.9940885) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8456466 4.2861584 4.6627256 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.455674 0.0000000) to (20.190194 49.455674 6.9940885) create_atoms CPU = 0.003 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8456466 4.2861584 4.6627256 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.455674 0.0000000) to (20.190194 49.455674 6.9940885) create_atoms CPU = 0.003 seconds 601 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1199 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_769582363439_005#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3715.4751 0 -3715.4751 197921.54 136 0 -4921.182 0 -4921.182 1396.3261 Loop time of 4.9828 on 1 procs for 136 steps with 1199 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3715.4751153357 -4921.17713058875 -4921.18197735574 Force two-norm initial, final = 2905.3277 0.29159974 Force max component initial, final = 768.88114 0.069812733 Final line search alpha, max atom move = 1.0000000 0.069812733 Iterations, force evaluations = 136 264 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8812 | 4.8812 | 4.8812 | 0.0 | 97.96 Neigh | 0.024568 | 0.024568 | 0.024568 | 0.0 | 0.49 Comm | 0.040051 | 0.040051 | 0.040051 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03701 | | | 0.74 Nlocal: 1199.00 ave 1199 max 1199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5946.00 ave 5946 max 5946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164306.0 ave 164306 max 164306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164306 Ave neighs/atom = 137.03586 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 136 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press Volume 136 0 -4921.182 0 -4921.182 1396.3261 13967.47 139 0 -4921.2118 0 -4921.2118 -4.5069184 13978.577 Loop time of 0.114143 on 1 procs for 3 steps with 1199 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4921.18197735572 -4921.21088260531 -4921.21180507299 Force two-norm initial, final = 35.523873 0.65198502 Force max component initial, final = 35.502559 0.42170637 Final line search alpha, max atom move = 0.00011087388 4.6756222e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11045 | 0.11045 | 0.11045 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077361 | 0.00077361 | 0.00077361 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002922 | | | 2.56 Nlocal: 1199.00 ave 1199 max 1199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5924.00 ave 5924 max 5924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164308.0 ave 164308 max 164308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164308 Ave neighs/atom = 137.03753 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.230 | 5.230 | 5.230 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4921.2118 0 -4921.2118 -4.5069184 Loop time of 6.415e-06 on 1 procs for 0 steps with 1199 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 1199.00 ave 1199 max 1199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5918.00 ave 5918 max 5918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164252.0 ave 164252 max 164252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164252 Ave neighs/atom = 136.99083 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.230 | 5.230 | 5.230 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 -4921.2118 -4921.2118 20.181415 99.079182 6.9908334 -4.5069184 -4.5069184 43.297061 -8.505777 -48.31204 2.2236183 646.15233 Loop time of 7.227e-06 on 1 procs for 0 steps with 1199 atoms 276.7% 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 | | 7.227e-06 | | |100.00 Nlocal: 1199.00 ave 1199 max 1199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5918.00 ave 5918 max 5918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82126.0 ave 82126 max 82126 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164252.0 ave 164252 max 164252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164252 Ave neighs/atom = 136.99083 Neighbor list builds = 0 Dangerous builds = 0 1199 -4921.21180507299 eV 2.22361827493499 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05