LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.081654928624631*${_u_distance} variable lattice_constant_converted equal 4.081654928624631*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 24.827737661444957*${_u_distance} variable xmax_converted equal 24.827737661444957*1 variable ymin_converted equal -49.65955697781854*${_u_distance} variable ymin_converted equal -49.65955697781854*1 variable ymax_converted equal 49.65955697781854*${_u_distance} variable ymax_converted equal 49.65955697781854*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.081654928624631*${_u_distance} variable zmax_converted equal 4.081654928624631*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.08165492862463 Lattice spacing in x,y,z = 4.08165 4.08165 4.08165 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 24.827737661445 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 24.827737661445 -49.6595569778185 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 24.827737661445 -49.6595569778185 49.6595569778185 ${zmin_converted} ${zmax_converted} units box region whole block 0 24.827737661445 -49.6595569778185 49.6595569778185 0 ${zmax_converted} units box region whole block 0 24.827737661445 -49.6595569778185 49.6595569778185 0 4.08165492862463 units box create_box 2 whole Created orthogonal box = (0 -49.6596 0) to (24.8277 49.6596 4.08165) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 49.6595569778185 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 6 -1 0 orient y 1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.69714 4.69714 4.08165 create_atoms 1 region upper Created 298 atoms create_atoms CPU = 0.000199795 secs group upper type 1 298 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.7372431386341987 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -49.6595569778185 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 lattice fcc 4.08165492862463 orient x 6 1 0 orient y -1 6 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.69714 4.69714 4.08165 create_atoms 2 region lower Created 298 atoms create_atoms CPU = 7.70092e-05 secs group lower type 2 298 atoms in group lower displace_atoms lower move -2.7372431386341987 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.08165492862463 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.04082746431231 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 17 1 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 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 586 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.366 | 5.366 | 5.366 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2087.4428 0 -2087.4428 -140.53609 219 0 -2092.6997 0 -2092.6997 -3834.0979 Loop time of 2.95352 on 1 procs for 219 steps with 586 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 = -2087.44275653 -2092.6996628 -2092.6996628 Force two-norm initial, final = 9.42901 1.27144e-05 Force max component initial, final = 3.42626 2.39097e-06 Final line search alpha, max atom move = 1 2.39097e-06 Iterations, force evaluations = 219 434 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9235 | 2.9235 | 2.9235 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022259 | 0.022259 | 0.022259 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007723 | | | 0.26 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9466 ave 9466 max 9466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248752 ave 248752 max 248752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248752 Ave neighs/atom = 424.491 Neighbor list builds = 0 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 5.367 | 5.367 | 5.367 Mbytes Step Temp E_pair E_mol TotEng Press Volume 219 0 -2092.6997 0 -2092.6997 -3834.0979 10064.826 1219 0 -2092.7395 0 -2092.7395 -576.56434 10028.971 Loop time of 15.0235 on 1 procs for 1000 steps with 586 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2092.6996628 -2092.7394675 -2092.7394675 Force two-norm initial, final = 31.4738 0.00650838 Force max component initial, final = 22.5404 0.00603003 Final line search alpha, max atom move = 1 0.00603003 Iterations, force evaluations = 1000 1999 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.636 | 14.636 | 14.636 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098671 | 0.098671 | 0.098671 | 0.0 | 0.66 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2884 | | | 1.92 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9501 ave 9501 max 9501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249172 ave 249172 max 249172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249172 Ave neighs/atom = 425.208 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 2.2204e-16 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.505 | 5.505 | 5.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2092.7395 0 -2092.7395 -576.56434 Loop time of 9.53674e-07 on 1 procs for 0 steps with 586 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9501 ave 9501 max 9501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249316 ave 249316 max 249316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249316 Ave neighs/atom = 425.454 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom 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 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 5.505 | 5.505 | 5.505 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 -2092.7395 -2092.7395 24.781115 99.319114 4.0747662 -576.56434 -576.56434 -0.96151751 -1728.5721 -0.15941281 2.4864153 301.93487 Loop time of 9.53674e-07 on 1 procs for 0 steps with 586 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9501 ave 9501 max 9501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124658 ave 124658 max 124658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249316 ave 249316 max 249316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249316 Ave neighs/atom = 425.454 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_018.9246/numatoms.out 586 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2092.73946750346-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2092.73946750346-586*${isolated_atom_energy} variable adjusted_pe_metal equal -2092.73946750346-586*2.2204e-16 print "${adjusted_pe_metal} eV" file output/dump_018.9246/energy.out -2092.73946750346 eV print "${mindist_metal} Angstroms" file output/dump_018.9246/mindistance.out 2.48641525548279 Angstroms write_dump all cfg output/dump_018.9246/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_018.9246/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18