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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -55.816520 0.0000000) to (32.225683 55.816520 5.4732601) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9577974 5.0091749 5.4732601 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -55.816520 0.0000000) to (32.225683 55.816520 5.4732601) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9577974 5.0091749 5.4732601 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -55.816520 0.0000000) to (32.225683 55.816520 5.4732601) create_atoms CPU = 0.001 seconds 628 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 10 34 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1248 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27642.949 0 -27642.949 39929.771 51 0 -27916.149 0 -27916.149 15906.326 Loop time of 39.5621 on 1 procs for 51 steps with 1248 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 = -27642.9490344317 -27916.1230021042 -27916.1488625482 Force two-norm initial, final = 227.38969 0.61151335 Force max component initial, final = 32.489229 0.10004455 Final line search alpha, max atom move = 0.60964619 0.060991781 Iterations, force evaluations = 51 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.539 | 39.539 | 39.539 | 0.0 | 99.94 Neigh | 0.0076012 | 0.0076012 | 0.0076012 | 0.0 | 0.02 Comm | 0.0083247 | 0.0083247 | 0.0083247 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007616 | | | 0.02 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5689.00 ave 5689 max 5689 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: 80472.0 ave 80472 max 80472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80472 Ave neighs/atom = 64.480769 Neighbor list builds = 1 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -27916.149 0 -27916.149 15906.326 19689.785 56 0 -27916.887 0 -27916.887 831.79207 19801.794 Loop time of 3.3928 on 1 procs for 5 steps with 1248 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 = -27916.1488625482 -27916.8760513601 -27916.8873592787 Force two-norm initial, final = 352.52395 20.612987 Force max component initial, final = 275.46457 18.299167 Final line search alpha, max atom move = 4.2127136e-05 0.00077089148 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3905 | 3.3905 | 3.3905 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037488 | 0.00037488 | 0.00037488 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001915 | | | 0.06 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5610.00 ave 5610 max 5610 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: 80296.0 ave 80296 max 80296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80296 Ave neighs/atom = 64.339744 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.788 | 4.788 | 4.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27916.887 0 -27916.887 831.79207 Loop time of 2.339e-06 on 1 procs for 0 steps with 1248 atoms 171.0% 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 | | 2.339e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603.00 ave 5603 max 5603 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: 80240.0 ave 80240 max 80240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80240 Ave neighs/atom = 64.294872 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.788 | 4.788 | 4.788 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 -27916.887 -27916.887 32.255591 112.11195 5.4758009 831.79207 831.79207 703.45221 1486.9497 304.97432 2.524939 665.03289 Loop time of 2.423e-06 on 1 procs for 0 steps with 1248 atoms 206.4% 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 | | 2.423e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5603.00 ave 5603 max 5603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40120.0 ave 40120 max 40120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80240.0 ave 80240 max 80240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80240 Ave neighs/atom = 64.294872 Neighbor list builds = 0 Dangerous builds = 0 1248 -6356.6941504595 eV 2.52493897955202 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:45