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 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 54.446810582854724*${_u_distance} variable xmax_converted equal 54.446810582854724*1 variable ymin_converted equal -54.45085758241353*${_u_distance} variable ymin_converted equal -54.45085758241353*1 variable ymax_converted equal 54.45085758241353*${_u_distance} variable ymax_converted equal 54.45085758241353*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 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 54.4468105828547 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.4468105828547 -54.4508575824135 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.4468105828547 -54.4508575824135 54.4508575824135 ${zmin_converted} ${zmax_converted} units box region whole block 0 54.4468105828547 -54.4508575824135 54.4508575824135 0 ${zmax_converted} units box region whole block 0 54.4468105828547 -54.4508575824135 54.4508575824135 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -54.4509 0) to (54.4468 54.4509 4.047) 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 54.4508575824135 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 10 -9 0 orient y 9 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71541 5.71541 4.047 create_atoms 1 region upper Created 725 atoms create_atoms CPU = 0.000243902 secs group upper type 1 725 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.054130821183169 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -54.4508575824135 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 9 0 orient y -9 10 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 10 9 0 orient y -9 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71541 5.71541 4.047 create_atoms 2 region lower Created 725 atoms create_atoms CPU = 0.000132084 secs group lower type 2 725 atoms in group lower displace_atoms lower move -6.054130821183169 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' 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*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 26 atoms, new total = 1424 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 13.35 | 13.35 | 13.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4742.6796 0 -4742.6796 -277.14612 320 0 -4771.0418 0 -4771.0418 -8989.8169 Loop time of 11.5712 on 1 procs for 320 steps with 1424 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 = -4742.67959815 -4771.0418249 -4771.0418249 Force two-norm initial, final = 16.5063 1.4614e-05 Force max component initial, final = 3.20029 4.67856e-06 Final line search alpha, max atom move = 1 4.67856e-06 Iterations, force evaluations = 320 627 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.518 | 11.518 | 11.518 | 0.0 | 99.54 Neigh | 0.010916 | 0.010916 | 0.010916 | 0.0 | 0.09 Comm | 0.02403 | 0.02403 | 0.02403 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01829 | | | 0.16 Nlocal: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7711 ave 7711 max 7711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60392 ave 60392 max 60392 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120784 ave 120784 max 120784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120784 Ave neighs/atom = 84.8202 Neighbor list builds = 3 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) = 13.35 | 13.35 | 13.35 Mbytes Step Temp E_pair E_mol TotEng Press Volume 320 0 -4771.0418 0 -4771.0418 -8989.8169 23996.081 1297 0 -4771.5478 0 -4771.5478 -2248.2138 23783.762 Loop time of 37.216 on 1 procs for 977 steps with 1424 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 = -4771.0418249 -4771.54775693 -4771.54775693 Force two-norm initial, final = 160.226 0.000451003 Force max component initial, final = 113.857 0.000220458 Final line search alpha, max atom move = 1 0.000220458 Iterations, force evaluations = 977 1950 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.899 | 36.899 | 36.899 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.071362 | 0.071362 | 0.071362 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2461 | | | 0.66 Nlocal: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7712 ave 7712 max 7712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60397 ave 60397 max 60397 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120794 ave 120794 max 120794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120794 Ave neighs/atom = 84.8272 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 0.0 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 16 31 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 12.23 | 12.23 | 12.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4771.5478 0 -4771.5478 -2248.2138 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1424 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 | | 1.192e-06 | | |100.00 Nlocal: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736 ave 7736 max 7736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60555 ave 60555 max 60555 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121110 ave 121110 max 121110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121110 Ave neighs/atom = 85.0492 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) = 12.23 | 12.23 | 12.23 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 -4771.5478 -4771.5478 54.20182 108.90172 4.0293218 -2248.2138 -2248.2138 0.014784152 -6744.6663 0.0099769342 2.4579568 638.77019 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1424 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: 1424 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7736 ave 7736 max 7736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60555 ave 60555 max 60555 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121110 ave 121110 max 121110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121110 Ave neighs/atom = 85.0492 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_083.9744/numatoms.out 1424 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4771.5477569334-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4771.5477569334-1424*${isolated_atom_energy} variable adjusted_pe_metal equal -4771.5477569334-1424*0 print "${adjusted_pe_metal} eV" file output/dump_083.9744/energy.out -4771.5477569334 eV print "${mindist_metal} Angstroms" file output/dump_083.9744/mindistance.out 2.45795678839006 Angstroms write_dump all cfg output/dump_083.9744/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_083.9744/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:48