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 Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -70.579301 0.0000000) to (40.746946 70.579301 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.579301 0.0000000) to (40.746946 70.579301 6.0968189) create_atoms CPU = 0.011 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734704 5.6179726 6.0968189 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.579301 0.0000000) to (40.746946 70.579301 6.0968189) create_atoms CPU = 0.010 seconds 1610 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 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 kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 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/MO_937008984446_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.840 | 5.840 | 5.840 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14118.555 0 -14118.555 2624.0742 40 0 -14164.647 0 -14164.647 -7275.0728 Loop time of 16.8361 on 1 procs for 40 steps with 3192 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 = -14118.5550134658 -14164.6379611861 -14164.6474940882 Force two-norm initial, final = 65.700812 0.32509730 Force max component initial, final = 15.963688 0.085326828 Final line search alpha, max atom move = 0.73473494 0.062692602 Iterations, force evaluations = 40 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.712 | 16.712 | 16.712 | 0.0 | 99.26 Neigh | 0.085798 | 0.085798 | 0.085798 | 0.0 | 0.51 Comm | 0.015848 | 0.015848 | 0.015848 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02241 | | | 0.13 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10254.0 ave 10254 max 10254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248312.0 ave 248312 max 248312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248312 Ave neighs/atom = 77.791980 Neighbor list builds = 2 Dangerous builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.840 | 5.840 | 5.840 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -14164.647 0 -14164.647 -7275.0728 35067.573 43 0 -14164.818 0 -14164.818 -2435.4535 34976.75 Loop time of 1.52009 on 1 procs for 3 steps with 3192 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 = -14164.6474940882 -14164.8178863986 -14164.8180501673 Force two-norm initial, final = 182.19010 0.37329088 Force max component initial, final = 145.15841 0.11235922 Final line search alpha, max atom move = 0.00030124102 3.3847207e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5133 | 1.5133 | 1.5133 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014623 | 0.0014623 | 0.0014623 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00533 | | | 0.35 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10254.0 ave 10254 max 10254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248372.0 ave 248372 max 248372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248372 Ave neighs/atom = 77.810777 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.978 | 5.978 | 5.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14164.818 0 -14164.818 -2435.4535 Loop time of 6.324e-06 on 1 procs for 0 steps with 3192 atoms 173.9% 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 | | 6.324e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10254.0 ave 10254 max 10254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248408.0 ave 248408 max 248408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248408 Ave neighs/atom = 77.822055 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.978 | 5.978 | 5.978 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 -14164.818 -14164.818 40.705006 141.1586 6.087294 -2435.4535 -2435.4535 -5.1415302 -7298.3108 -2.908097 2.2484313 1064.0463 Loop time of 6.686e-06 on 1 procs for 0 steps with 3192 atoms 329.0% 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 | | 6.686e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10254.0 ave 10254 max 10254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124204.0 ave 124204 max 124204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248408.0 ave 248408 max 248408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248408 Ave neighs/atom = 77.822055 Neighbor list builds = 0 Dangerous builds = 0 3192 -14164.8180501673 eV 2.24843127962974 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19