LAMMPS (23 Jun 2022) 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_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created orthogonal box = (0 -48.57515 0) to (24.287575 48.57515 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7147235 5.7147235 4.1652847 Created 271 atoms using lattice units in orthogonal box = (0 -48.57515 0) to (24.287575 48.57515 4.1652847) create_atoms CPU = 0.000 seconds 271 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7147235 5.7147235 4.1652847 Created 273 atoms using lattice units in orthogonal box = (0 -48.57515 0) to (24.287575 48.57515 4.1652847) create_atoms CPU = 0.000 seconds 273 atoms in group lower Displacing atoms ... WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXw8YPNF/ffield.reax.AuO with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off pair build: copy stencil: none bin: none Deleted 0 atoms, new total = 544 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_974345878378_001#item-citation - pair reaxff command: - fix qeq/reaxff command: 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:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 17 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 301.3 | 301.3 | 301.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -43725.947 0 -43725.947 41244.557 68 0 -46688.509 0 -46688.509 13054.157 Loop time of 8.73064 on 1 procs for 68 steps with 544 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 = -43725.9471842286 -46688.4752986399 -46688.5086744663 Force two-norm initial, final = 4163.4741 3.1337718 Force max component initial, final = 1022.7665 0.84930054 Final line search alpha, max atom move = 0.16715933 0.14196851 Iterations, force evaluations = 68 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0677 | 7.0677 | 7.0677 | 0.0 | 80.95 Neigh | 0.083139 | 0.083139 | 0.083139 | 0.0 | 0.95 Comm | 0.0052991 | 0.0052991 | 0.0052991 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.5719 | 1.5719 | 1.5719 | 0.0 | 18.00 Other | | 0.002617 | | | 0.03 Nlocal: 544 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8878 ave 8878 max 8878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187292 ave 187292 max 187292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187292 Ave neighs/atom = 344.28676 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : real Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 301.3 | 301.3 | 301.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -46688.509 0 -46688.509 13054.157 9828.1775 79 0 -46704.939 0 -46704.939 -49.918543 9920.3059 Loop time of 0.87848 on 1 procs for 11 steps with 544 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 = -46688.5086744311 -46704.9326075534 -46704.9386537818 Force two-norm initial, final = 3834.4439 17.710126 Force max component initial, final = 3469.1181 10.145357 Final line search alpha, max atom move = 2.3511689e-05 0.00023853448 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78618 | 0.78618 | 0.78618 | 0.0 | 89.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047574 | 0.00047574 | 0.00047574 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.090281 | 0.090281 | 0.090281 | 0.0 | 10.28 Other | | 0.001539 | | | 0.18 Nlocal: 544 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8878 ave 8878 max 8878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186236 ave 186236 max 186236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186236 Ave neighs/atom = 342.34559 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 17 1 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/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 (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301.4 | 301.4 | 301.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -46704.939 0 -46704.939 -49.918544 Loop time of 8.82e-07 on 1 procs for 0 steps with 544 atoms 340.1% 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 | | 8.82e-07 | | |100.00 Nlocal: 544 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8822 ave 8822 max 8822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 185717 ave 185717 max 185717 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185717 Ave neighs/atom = 341.39154 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 301.4 | 301.4 | 301.4 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 -2025.3178 -46704.939 24.271682 98.08218 4.1671111 -49.918544 -50.579965 -71.006602 -47.805082 -32.928211 2.7048938 410.07242 Loop time of 1.002e-06 on 1 procs for 0 steps with 544 atoms 598.8% 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 | | 1.002e-06 | | |100.00 Nlocal: 544 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8822 ave 8822 max 8822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 185717 ave 185717 max 185717 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206038 ave 206038 max 206038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206038 Ave neighs/atom = 378.74632 Neighbor list builds = 0 Dangerous builds = 0 544 -2025.31781244273 eV 2.70489376853055 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:36