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_XuWangQian_2022_NiPd__SM_559286646876_000 # For Simulator : LAMMPS 29 Sep 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5239994 3.5239994 3.5239994 Created orthogonal box = (0.0000000 -36.622476 0.0000000) to (8.6320004 36.622476 4.9836877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7546669 6.1037460 4.9836877 Created 143 atoms using lattice units in orthogonal box = (0.0000000 -36.622476 0.0000000) to (8.6320004 36.622476 4.9836877) create_atoms CPU = 0.001 seconds 143 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7546669 6.1037460 4.9836877 Created 151 atoms using lattice units in orthogonal box = (0.0000000 -36.622476 0.0000000) to (8.6320004 36.622476 4.9836877) create_atoms CPU = 0.001 seconds 151 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 = 2 17 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 6 atoms, new total = 288 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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 2 17 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) = 7.113 | 7.113 | 7.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1278.1284 0 -1278.1284 371.17765 24 0 -1278.5071 0 -1278.5071 -187.96406 Loop time of 0.278703 on 1 procs for 24 steps with 288 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 = -1278.12839576782 -1278.50639015685 -1278.50710732946 Force two-norm initial, final = 2.3615328 0.074369110 Force max component initial, final = 1.3628928 0.010343502 Final line search alpha, max atom move = 1.0000000 0.010343502 Iterations, force evaluations = 24 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27562 | 0.27562 | 0.27562 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020007 | 0.0020007 | 0.0020007 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001086 | | | 0.39 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36100.0 ave 36100 max 36100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36100 Ave neighs/atom = 125.34722 Neighbor list builds = 0 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.113 | 7.113 | 7.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -1278.5071 0 -1278.5071 -187.96406 3150.9388 25 0 -1278.5071 0 -1278.5071 2.5643733 3150.6173 Loop time of 0.0159621 on 1 procs for 1 steps with 288 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 = -1278.50710732946 -1278.50710732946 -1278.50712674237 Force two-norm initial, final = 0.64792653 0.082225676 Force max component initial, final = 0.40633047 0.031838176 Final line search alpha, max atom move = 0.0024610510 7.8355376e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015539 | 0.015539 | 0.015539 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010718 | 0.00010718 | 0.00010718 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003155 | | | 1.98 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36000.0 ave 36000 max 36000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36000 Ave neighs/atom = 125.00000 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 = 8.8996314 ghost atom cutoff = 8.8996314 binsize = 4.4498157, bins = 2 17 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) = 6.744 | 6.744 | 6.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1278.5071 0 -1278.5071 2.5643733 Loop time of 1.828e-06 on 1 procs for 0 steps with 288 atoms 164.1% 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 | | 1.828e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36000.0 ave 36000 max 36000 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 = 36000 Ave neighs/atom = 125.00000 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) = 6.744 | 6.744 | 6.744 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 -1278.5071 -1278.5071 8.6316944 73.242814 4.9835014 2.5643733 2.5643733 -0.94618761 16.190125 -7.5508175 2.4889136 99.257227 Loop time of 2.276e-06 on 1 procs for 0 steps with 288 atoms 175.7% 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 | | 2.276e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36000.0 ave 36000 max 36000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72000.0 ave 72000 max 72000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72000 Ave neighs/atom = 250.00000 Neighbor list builds = 0 Dangerous builds = 0 288 -1278.50712674237 eV 2.48891364666405 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00