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_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 # For Simulator : LAMMPS 22 Sep 2017 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5765109 4.4360873 4.9780317 Created 812 atoms using lattice units in orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) create_atoms CPU = 0.005 seconds 812 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5765109 4.4360873 4.9780317 Created 820 atoms using lattice units in orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) create_atoms CPU = 0.004 seconds 820 atoms in group lower Displacing atoms ... Reading adp potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXX65c9fw/Ni.adp with DATE: 2011-06-20 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 10 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 0 atoms, new total = 1632 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_477692857359_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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 10 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) = 7.894 | 7.894 | 7.894 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7162.7125 0 -7162.7125 5458.1602 48 0 -7237.7843 0 -7237.7843 7585.1434 Loop time of 2.60917 on 1 procs for 48 steps with 1632 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 = -7162.71249186435 -7237.77785464815 -7237.7842620362 Force two-norm initial, final = 27.776630 0.27031608 Force max component initial, final = 4.2911585 0.018597943 Final line search alpha, max atom move = 1.0000000 0.018597943 Iterations, force evaluations = 48 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5592 | 2.5592 | 2.5592 | 0.0 | 98.08 Neigh | 0.01394 | 0.01394 | 0.01394 | 0.0 | 0.53 Comm | 0.019312 | 0.019312 | 0.019312 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01673 | | | 0.64 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8840.00 ave 8840 max 8840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113834.0 ave 113834 max 113834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113834 Ave neighs/atom = 69.751225 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.894 | 7.894 | 7.894 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -7237.7843 0 -7237.7843 7585.1434 17794.597 52 0 -7238.019 0 -7238.019 -331.13881 17873.052 Loop time of 0.172381 on 1 procs for 4 steps with 1632 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 = -7237.7842620362 -7238.01647616775 -7238.01897593629 Force two-norm initial, final = 153.54378 7.1518340 Force max component initial, final = 107.07353 6.0686645 Final line search alpha, max atom move = 8.8067854e-05 0.00053445426 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1672 | 0.1672 | 0.1672 | 0.0 | 96.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011968 | 0.0011968 | 0.0011968 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003986 | | | 2.31 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8832.00 ave 8832 max 8832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113754.0 ave 113754 max 113754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113754 Ave neighs/atom = 69.702206 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 = 7.168 ghost atom cutoff = 7.168 binsize = 3.584, bins = 10 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) = 7.525 | 7.525 | 7.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7238.019 0 -7238.019 -331.13881 Loop time of 6.365e-06 on 1 procs for 0 steps with 1632 atoms 188.5% 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: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8832.00 ave 8832 max 8832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113712.0 ave 113712 max 113712 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 = 113712 Ave neighs/atom = 69.676471 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) = 7.525 | 7.525 | 7.525 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 -7238.019 -7238.019 35.536631 100.8701 4.9860891 -331.13881 -331.13881 -307.19697 -141.33159 -544.88787 2.3307384 769.80721 Loop time of 7.146e-06 on 1 procs for 0 steps with 1632 atoms 223.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8832.00 ave 8832 max 8832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113712.0 ave 113712 max 113712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227424.0 ave 227424 max 227424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227424 Ave neighs/atom = 139.35294 Neighbor list builds = 0 Dangerous builds = 0 1632 -7238.01897593629 eV 2.33073835345549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03