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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_PunDarlingKecskes_2015_CuTa__SM_399364650444_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -44.274529 0.0000000) to (6.2613639 44.274529 5.1123822) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2613639 5.9032705 5.1123822 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.274529 0.0000000) to (6.2613639 44.274529 5.1123822) create_atoms CPU = 0.002 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2613639 5.9032705 5.1123822 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.274529 0.0000000) to (6.2613639 44.274529 5.1123822) create_atoms CPU = 0.002 seconds 122 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 2 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 240 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/SM_399364650444_000#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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.091 | 7.091 | 7.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -823.19151 0 -823.19151 37421.787 85 0 -847.21192 0 -847.21192 3437.7976 Loop time of 1.14074 on 1 procs for 85 steps with 240 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 = -823.191509625972 -847.211101452654 -847.211915682696 Force two-norm initial, final = 60.690149 0.083069407 Force max component initial, final = 22.520606 0.022419264 Final line search alpha, max atom move = 1.0000000 0.022419264 Iterations, force evaluations = 85 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1116 | 1.1116 | 1.1116 | 0.0 | 97.45 Neigh | 0.0029315 | 0.0029315 | 0.0029315 | 0.0 | 0.26 Comm | 0.016243 | 0.016243 | 0.016243 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00994 | | | 0.87 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4155.00 ave 4155 max 4155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23616.0 ave 23616 max 23616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23616 Ave neighs/atom = 98.400000 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.091 | 7.091 | 7.091 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -847.21192 0 -847.21192 3437.7976 2834.4983 89 0 -847.23179 0 -847.23179 -44.576376 2841.5562 Loop time of 0.042888 on 1 procs for 4 steps with 240 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -847.211915682696 -847.231701264958 -847.231790775385 Force two-norm initial, final = 13.285786 0.18655319 Force max component initial, final = 12.359984 0.12841606 Final line search alpha, max atom move = 0.0021189517 0.00027210744 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040912 | 0.040912 | 0.040912 | 0.0 | 95.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050475 | 0.00050475 | 0.00050475 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001471 | | | 3.43 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3944.00 ave 3944 max 3944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23704.0 ave 23704 max 23704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23704 Ave neighs/atom = 98.766667 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 = 8.150959 ghost atom cutoff = 8.150959 binsize = 4.0754795, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.720 | 6.720 | 6.720 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -847.23179 0 -847.23179 -44.576376 Loop time of 6.365e-06 on 1 procs for 0 steps with 240 atoms 157.1% 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 | | 6.365e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23692.0 ave 23692 max 23692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23692 Ave neighs/atom = 98.716667 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) = 6.720 | 6.720 | 6.720 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 -847.23179 -847.23179 6.2811977 88.445697 5.1148991 -44.576376 -44.576376 -72.635174 -53.494435 -7.5995187 2.4198276 191.40374 Loop time of 6.765e-06 on 1 procs for 0 steps with 240 atoms 266.1% 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 | | 6.765e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23692.0 ave 23692 max 23692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47384.0 ave 47384 max 47384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47384 Ave neighs/atom = 197.43333 Neighbor list builds = 0 Dangerous builds = 0 240 -847.231790775385 eV 2.41982758688682 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01