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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -40.303825 0.0000000) to (20.151912 40.303825 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4235905 4.4235905 3.1472000 Created 164 atoms using lattice units in orthogonal box = (0.0000000 -40.303825 0.0000000) to (20.151912 40.303825 3.1472000) create_atoms CPU = 0.002 seconds 164 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4235905 4.4235905 3.1472000 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -40.303825 0.0000000) to (20.151912 40.303825 3.1472000) create_atoms CPU = 0.001 seconds 165 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 26 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 329 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2064.2763 0 -2064.2763 107047.53 55 0 -2231.4149 0 -2231.4149 10981.407 Loop time of 0.41396 on 1 procs for 55 steps with 329 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2064.27628620052 -2231.41289231524 -2231.41492126705 Force two-norm initial, final = 334.95132 0.18427792 Force max component initial, final = 129.73799 0.040659287 Final line search alpha, max atom move = 1.0000000 0.040659287 Iterations, force evaluations = 55 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40103 | 0.40103 | 0.40103 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069169 | 0.0069169 | 0.0069169 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006015 | | | 1.45 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2746.00 ave 2746 max 2746 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: 19338.0 ave 19338 max 19338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19338 Ave neighs/atom = 58.778116 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -2231.4149 0 -2231.4149 10981.407 5112.3063 62 0 -2231.6687 0 -2231.6687 -156.01089 5130.3043 Loop time of 0.0358817 on 1 procs for 7 steps with 329 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2231.41492126705 -2231.66857936102 -2231.6686990441 Force two-norm initial, final = 86.579383 0.99581100 Force max component initial, final = 81.599922 0.53326051 Final line search alpha, max atom move = 0.00098844263 0.00052709742 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033365 | 0.033365 | 0.033365 | 0.0 | 92.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056906 | 0.00056906 | 0.00056906 | 0.0 | 1.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001948 | | | 5.43 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2746.00 ave 2746 max 2746 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: 19368.0 ave 19368 max 19368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19368 Ave neighs/atom = 58.869301 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2231.6687 0 -2231.6687 -156.01089 Loop time of 6.485e-06 on 1 procs for 0 steps with 329 atoms 138.8% 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 | | 6.485e-06 | | |100.00 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2750.00 ave 2750 max 2750 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: 19312.0 ave 19312 max 19312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19312 Ave neighs/atom = 58.699088 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.554 | 4.554 | 4.554 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 -2231.6687 -2231.6687 20.154275 81.096252 3.1388832 -156.01089 -156.01089 -166.55496 -155.78701 -145.69071 2.5145482 187.14477 Loop time of 6.485e-06 on 1 procs for 0 steps with 329 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2750.00 ave 2750 max 2750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9656.00 ave 9656 max 9656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19312.0 ave 19312 max 19312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19312 Ave neighs/atom = 58.699088 Neighbor list builds = 0 Dangerous builds = 0 329 -2231.6686990441 eV 2.51454818486773 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42