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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6690360 5.7277840 6.2584463 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.008 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6690360 5.7277840 6.2584463 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.007 seconds 1251 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 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 kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8707.5515 0 -8707.5515 4611.5371 33 0 -8749.4554 0 -8749.4554 -3228.2025 Loop time of 12.0982 on 1 procs for 33 steps with 2480 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 = -8707.55152669243 -8749.4474689559 -8749.45539831203 Force two-norm initial, final = 63.663006 0.30812305 Force max component initial, final = 11.009604 0.081353717 Final line search alpha, max atom move = 1.0000000 0.081353717 Iterations, force evaluations = 33 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.066 | 12.066 | 12.066 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01619 | 0.01619 | 0.01619 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01608 | | | 0.13 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10075.0 ave 10075 max 10075 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: 327704.0 ave 327704 max 327704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327704 Ave neighs/atom = 132.13871 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -8749.4554 0 -8749.4554 -3228.2025 29439.259 35 0 -8749.511 0 -8749.511 -733.02724 29386.923 Loop time of 0.7045 on 1 procs for 2 steps with 2480 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8749.45539831205 -8749.50555370673 -8749.51103194649 Force two-norm initial, final = 76.725978 8.1002915 Force max component initial, final = 71.598535 7.8694445 Final line search alpha, max atom move = 5.0342991e-05 0.00039617138 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70058 | 0.70058 | 0.70058 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085523 | 0.00085523 | 0.00085523 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003061 | | | 0.43 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10075.0 ave 10075 max 10075 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: 322476.0 ave 322476 max 322476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322476 Ave neighs/atom = 130.03065 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.251 | 6.251 | 6.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8749.511 0 -8749.511 -733.02724 Loop time of 4.0844e-05 on 1 procs for 0 steps with 2480 atoms 29.4% 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 | | 4.084e-05 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10075.0 ave 10075 max 10075 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: 322954.0 ave 322954 max 322954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322954 Ave neighs/atom = 130.22339 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.251 | 6.251 | 6.251 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 -8749.511 -8749.511 36.839206 127.65499 6.2489359 -733.02724 -733.02724 428.93157 -2731.0895 103.07616 2.2905847 1056.9997 Loop time of 7.007e-06 on 1 procs for 0 steps with 2480 atoms 285.4% 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 | | 7.007e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10075.0 ave 10075 max 10075 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 161477.0 ave 161477 max 161477 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 322954.0 ave 322954 max 322954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322954 Ave neighs/atom = 130.22339 Neighbor list builds = 0 Dangerous builds = 0 2480 -8749.51103194649 eV 2.29058465253402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14