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_ADP_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.8900001 3.8900001 3.8900001 Created orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0944588 6.7035627 5.5012908 Created 528 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0944588 6.7035627 5.5012908 Created 530 atoms using lattice units in orthogonal box = (0 -63.20502 0) to (22.346349 63.20502 5.5012908) create_atoms CPU = 0.001 seconds 530 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 29 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 = 1056 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_559286646876_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:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 29 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) = 7.772 | 7.772 | 7.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3534.0632 0 -3534.0632 101187.61 110 0 -4098.3488 0 -4098.3488 4193.0213 Loop time of 1.17498 on 1 procs for 110 steps with 1056 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3534.06318504286 -4098.34591695169 -4098.34882878742 Force two-norm initial, final = 876.43853 0.18570616 Force max component initial, final = 267.51345 0.047385371 Final line search alpha, max atom move = 1 0.047385371 Iterations, force evaluations = 110 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1627 | 1.1627 | 1.1627 | 0.0 | 98.96 Neigh | 0.0022664 | 0.0022664 | 0.0022664 | 0.0 | 0.19 Comm | 0.0063137 | 0.0063137 | 0.0063137 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003676 | | | 0.31 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8153 ave 8153 max 8153 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105170 ave 105170 max 105170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105170 Ave neighs/atom = 99.592803 Neighbor list builds = 1 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 : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.772 | 7.772 | 7.772 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -4098.3488 0 -4098.3488 4193.0213 15540.062 114 0 -4098.4863 0 -4098.4863 -477.12412 15576.013 Loop time of 0.0333133 on 1 procs for 4 steps with 1056 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4098.34882878742 -4098.48296106739 -4098.48628603083 Force two-norm initial, final = 87.384515 10.189166 Force max component initial, final = 82.595887 8.8493933 Final line search alpha, max atom move = 7.3672023e-05 0.00065195271 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032609 | 0.032609 | 0.032609 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016099 | 0.00016099 | 0.00016099 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005432 | | | 1.63 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616 ave 7616 max 7616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105274 ave 105274 max 105274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105274 Ave neighs/atom = 99.691288 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: 2000, page size: 100000 master list distance cutoff = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 6 29 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) = 7.4 | 7.4 | 7.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4098.4863 0 -4098.4863 -477.12412 Loop time of 6.52e-07 on 1 procs for 0 steps with 1056 atoms 153.4% 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 | | 6.52e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616 ave 7616 max 7616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105264 ave 105264 max 105264 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 = 105264 Ave neighs/atom = 99.681818 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 : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.4 | 7.4 | 7.4 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 -4098.4863 -4098.4863 22.324631 126.84662 5.5003854 -477.12412 -477.12412 -909.37973 -3.1735303 -518.81911 2.5616913 432.27406 Loop time of 5.81e-07 on 1 procs for 0 steps with 1056 atoms 344.2% 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 | | 5.81e-07 | | |100.00 Nlocal: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616 ave 7616 max 7616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105264 ave 105264 max 105264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210528 ave 210528 max 210528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210528 Ave neighs/atom = 199.36364 Neighbor list builds = 0 Dangerous builds = 0 1056 -4098.48628603083 eV 2.56169129795118 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01