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 -54.146476 0.0000000) to (27.073238 54.146476 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3902548 4.3902548 3.1472000 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -54.146476 0.0000000) to (27.073238 54.146476 3.1472000) create_atoms CPU = 0.002 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3902548 4.3902548 3.1472000 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -54.146476 0.0000000) to (27.073238 54.146476 3.1472000) create_atoms CPU = 0.001 seconds 298 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 = 9 35 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 2 atoms, new total = 592 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 = 9 35 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) = 4.483 | 4.483 | 4.483 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3402.6584 0 -3402.6584 104412.28 174 0 -4017.7803 0 -4017.7803 7777.9642 Loop time of 2.21705 on 1 procs for 174 steps with 592 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 = -3402.65844105372 -4017.77636328324 -4017.78031043313 Force two-norm initial, final = 781.10060 0.32276934 Force max component initial, final = 206.00719 0.038449012 Final line search alpha, max atom move = 1.0000000 0.038449012 Iterations, force evaluations = 174 337 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1454 | 2.1454 | 2.1454 | 0.0 | 96.77 Neigh | 0.013308 | 0.013308 | 0.013308 | 0.0 | 0.60 Comm | 0.031116 | 0.031116 | 0.031116 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02719 | | | 1.23 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4228.00 ave 4228 max 4228 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: 34632.0 ave 34632 max 34632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34632 Ave neighs/atom = 58.500000 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 35 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 : 174 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.483 | 4.483 | 4.483 Mbytes Step Temp E_pair E_mol TotEng Press Volume 174 0 -4017.7803 0 -4017.7803 7777.9642 9227.0894 180 0 -4018.0313 0 -4018.0313 86.748088 9250.7035 Loop time of 0.0600461 on 1 procs for 6 steps with 592 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 = -4017.78031043313 -4018.03127088958 -4018.03134634332 Force two-norm initial, final = 112.45628 1.2404104 Force max component initial, final = 107.86559 0.99184738 Final line search alpha, max atom move = 0.00048931503 0.00048532584 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05665 | 0.05665 | 0.05665 | 0.0 | 94.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076575 | 0.00076575 | 0.00076575 | 0.0 | 1.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00263 | | | 4.38 Nlocal: 592.000 ave 592 max 592 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: 34628.0 ave 34628 max 34628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34628 Ave neighs/atom = 58.493243 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 = 9 35 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) = 4.621 | 4.621 | 4.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4018.0313 0 -4018.0313 86.748088 Loop time of 9.091e-06 on 1 procs for 0 steps with 592 atoms 154.0% 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 | | 9.091e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4223.00 ave 4223 max 4223 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: 34572.0 ave 34572 max 34572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34572 Ave neighs/atom = 58.398649 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 = 9 35 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) = 4.621 | 4.621 | 4.621 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 -4018.0313 -4018.0313 27.066218 108.79865 3.1414032 86.748088 86.748088 4.8482545 83.929309 171.4667 2.5344886 400.74813 Loop time of 2.2572e-05 on 1 procs for 0 steps with 592 atoms 70.9% 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 | | 2.257e-05 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4223.00 ave 4223 max 4223 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17286.0 ave 17286 max 17286 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34572.0 ave 34572 max 34572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34572 Ave neighs/atom = 58.398649 Neighbor list builds = 0 Dangerous builds = 0 592 -4018.03134634332 eV 2.53448857294938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42