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 -58.371864 0.0000000) to (20.637570 58.371864 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2793785 5.4299408 4.4508129 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -58.371864 0.0000000) to (20.637570 58.371864 4.4508129) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2793785 5.4299408 4.4508129 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -58.371864 0.0000000) to (20.637570 58.371864 4.4508129) create_atoms CPU = 0.001 seconds 346 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 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 690 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 38 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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4484.2341 0 -4484.2341 81956.199 73 0 -4680.7565 0 -4680.7565 12591.121 Loop time of 0.417279 on 1 procs for 73 steps with 690 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4484.23413102183 -4680.75183669191 -4680.75648500975 Force two-norm initial, final = 293.33373 0.30483388 Force max component initial, final = 95.505772 0.044576467 Final line search alpha, max atom move = 1.0000000 0.044576467 Iterations, force evaluations = 73 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40838 | 0.40838 | 0.40838 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047336 | 0.0047336 | 0.0047336 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004162 | | | 1.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4210.00 ave 4210 max 4210 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: 40404.0 ave 40404 max 40404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40404 Ave neighs/atom = 58.556522 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 38 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -4680.7565 0 -4680.7565 12591.121 10723.374 79 0 -4681.0871 0 -4681.0871 -8.1365756 10769.07 Loop time of 0.0306079 on 1 procs for 6 steps with 690 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 = -4680.75648500975 -4681.08685479175 -4681.08714947679 Force two-norm initial, final = 163.51176 0.69700294 Force max component initial, final = 144.18288 0.14235819 Final line search alpha, max atom move = 0.00019585996 2.7882269e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028704 | 0.028704 | 0.028704 | 0.0 | 93.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031443 | 0.00031443 | 0.00031443 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001589 | | | 5.19 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4218.00 ave 4218 max 4218 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: 40292.0 ave 40292 max 40292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40292 Ave neighs/atom = 58.394203 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 38 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) = 4.660 | 4.660 | 4.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4681.0871 0 -4681.0871 -8.1365756 Loop time of 1.698e-06 on 1 procs for 0 steps with 690 atoms 176.7% 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 | | 1.698e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4218.00 ave 4218 max 4218 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: 40256.0 ave 40256 max 40256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40256 Ave neighs/atom = 58.342029 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 38 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) = 4.660 | 4.660 | 4.660 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 -4681.0871 -4681.0871 20.6253 117.30666 4.450976 -8.1365756 -8.1365756 -17.458372 -15.645307 8.6939525 2.4003892 408.56756 Loop time of 2.065e-06 on 1 procs for 0 steps with 690 atoms 193.7% 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 | | 2.065e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4218.00 ave 4218 max 4218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20128.0 ave 20128 max 20128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40256.0 ave 40256 max 40256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40256 Ave neighs/atom = 58.342029 Neighbor list builds = 0 Dangerous builds = 0 690 -4681.08714947679 eV 2.4003892425271 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