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 43.020195414185025*${_u_distance} variable xmax_converted equal 43.020195414185025*1 variable ymin_converted equal -43.024242413743835*${_u_distance} variable ymin_converted equal -43.024242413743835*1 variable ymax_converted equal 43.024242413743835*${_u_distance} variable ymax_converted equal 43.024242413743835*1 variable zmin_converted equal 0.0*${_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 43.020195414185 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 43.020195414185 -43.0242424137438 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 43.020195414185 -43.0242424137438 43.0242424137438 ${zmin_converted} ${zmax_converted} units box region whole block 0 43.020195414185 -43.0242424137438 43.0242424137438 0 ${zmax_converted} units box region whole block 0 43.020195414185 -43.0242424137438 43.0242424137438 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -43.0242 0) to (43.0202 43.0242 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 43.0242424137438 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 8 -7 0 orient y 7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71065 5.71065 4.047 create_atoms 1 region upper Created 454 atoms create_atoms CPU = 0.000209808 secs group upper type 1 454 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.783565615730593 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -43.0242424137438 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 8 7 0 orient y -7 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71065 5.71065 4.047 create_atoms 2 region lower Created 454 atoms create_atoms CPU = 8.79765e-05 secs group lower type 2 454 atoms in group lower displace_atoms lower move -4.783565615730593 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 13 25 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 20 atoms, new total = 888 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 = 13 25 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) = 11.83 | 11.83 | 11.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2949.4898 0 -2949.4898 1047.1207 246 0 -2972.0309 0 -2972.0309 -8807.2607 Loop time of 5.19283 on 1 procs for 246 steps with 888 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 = -2949.48980068 -2972.03087015 -2972.03087015 Force two-norm initial, final = 21.6751 4.37777e-06 Force max component initial, final = 4.57993 7.336e-07 Final line search alpha, max atom move = 1 7.336e-07 Iterations, force evaluations = 246 477 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1679 | 5.1679 | 5.1679 | 0.0 | 99.52 Neigh | 0.0040169 | 0.0040169 | 0.0040169 | 0.0 | 0.08 Comm | 0.012196 | 0.012196 | 0.012196 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008763 | | | 0.17 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5291 ave 5291 max 5291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37522 ave 37522 max 37522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75044 ave 75044 max 75044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75044 Ave neighs/atom = 84.509 Neighbor list builds = 2 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) = 11.83 | 11.83 | 11.83 Mbytes Step Temp E_pair E_mol TotEng Press Volume 246 0 -2972.0309 0 -2972.0309 -8807.2607 14981.275 1246 0 -2972.3456 0 -2972.3456 -2190.2284 14850.317 Loop time of 22.743 on 1 procs for 1000 steps with 888 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2972.03087015 -2972.3455524 -2972.3455524 Force two-norm initial, final = 97.9511 0.000893819 Force max component initial, final = 76.1089 0.000742371 Final line search alpha, max atom move = 1 0.000742371 Iterations, force evaluations = 1000 1995 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.53 | 22.53 | 22.53 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.049329 | 0.049329 | 0.049329 | 0.0 | 0.22 Output | 1.4782e-05 | 1.4782e-05 | 1.4782e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1639 | | | 0.72 Nlocal: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5308 ave 5308 max 5308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37580 ave 37580 max 37580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75160 ave 75160 max 75160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75160 Ave neighs/atom = 84.6396 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 = 13 25 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) = 10.71 | 10.71 | 10.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2972.3456 0 -2972.3456 -2190.2284 Loop time of 1.19209e-06 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5326 ave 5326 max 5326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37650 ave 37650 max 37650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75300 ave 75300 max 75300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75300 Ave neighs/atom = 84.7973 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) = 10.71 | 10.71 | 10.71 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 -2972.3456 -2972.3456 42.769493 86.048485 4.035138 -2190.2284 -2190.2284 -0.079626435 -6570.6004 -0.0051889484 2.5613907 596.68789 Loop time of 9.53674e-07 on 1 procs for 0 steps with 888 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: 888 ave 888 max 888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5326 ave 5326 max 5326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37650 ave 37650 max 37650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75300 ave 75300 max 75300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75300 Ave neighs/atom = 84.7973 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_082.3719/numatoms.out 888 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2972.34555240122-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2972.34555240122-888*${isolated_atom_energy} variable adjusted_pe_metal equal -2972.34555240122-888*0 print "${adjusted_pe_metal} eV" file output/dump_082.3719/energy.out -2972.34555240122 eV print "${mindist_metal} Angstroms" file output/dump_082.3719/mindistance.out 2.56139074170262 Angstroms write_dump all cfg output/dump_082.3719/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_082.3719/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:28