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 4.066269248723984*${_u_distance} variable lattice_constant_converted equal 4.066269248723984*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 53.48342163081442*${_u_distance} variable xmax_converted equal 53.48342163081442*1 variable ymin_converted equal -53.487487900063144*${_u_distance} variable ymin_converted equal -53.487487900063144*1 variable ymax_converted equal 53.487487900063144*${_u_distance} variable ymax_converted equal 53.487487900063144*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.066269248723984*${_u_distance} variable zmax_converted equal 4.066269248723984*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06626924872398 Lattice spacing in x,y,z = 4.06627 4.06627 4.06627 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 53.4834216308144 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4834216308144 -53.4874879000631 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4834216308144 -53.4874879000631 53.4874879000631 ${zmin_converted} ${zmax_converted} units box region whole block 0 53.4834216308144 -53.4874879000631 53.4874879000631 0 ${zmax_converted} units box region whole block 0 53.4834216308144 -53.4874879000631 53.4874879000631 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -53.4875 0) to (53.4834 53.4875 4.06627) 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 53.4874879000631 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 13 -2 0 orient y 2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.63729 4.63729 4.06627 create_atoms 1 region upper Created 694 atoms create_atoms CPU = 0.000210762 secs group upper type 1 694 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.918825897084657 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -53.4874879000631 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 13 2 0 orient y -2 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.63729 4.63729 4.06627 create_atoms 2 region lower Created 694 atoms create_atoms CPU = 0.000101089 secs group lower type 2 694 atoms in group lower displace_atoms lower move -5.918825897084657 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style bop pair_coeff * * ./SM_566399258279_000-files/b'AlCu.bop.table' Al Al Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 comm_modify cutoff 12.7 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*4.06626924872398 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03313462436199 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 18 35 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 24 atoms, new total = 1364 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.58 | 13.58 | 13.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4546.4193 0 -4546.4193 -10537.401 254 0 -4563.8211 0 -4563.8211 -15733.798 Loop time of 41.5749 on 1 procs for 254 steps with 1364 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 = -4546.41925272 -4563.8211199 -4563.8211199 Force two-norm initial, final = 7.97616 0.00708529 Force max component initial, final = 1.68237 0.00345787 Final line search alpha, max atom move = 0.5 0.00172893 Iterations, force evaluations = 254 513 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 41.497 | 41.497 | 41.497 | 0.0 | 99.81 Neigh | 0.026504 | 0.026504 | 0.026504 | 0.0 | 0.06 Comm | 0.037276 | 0.037276 | 0.037276 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01393 | | | 0.03 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15996 ave 15996 max 15996 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: 73596 ave 73596 max 73596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73596 Ave neighs/atom = 53.956 Neighbor list builds = 1 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) = 13.6 | 13.6 | 13.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 254 0 -4563.8211 0 -4563.8211 -15733.798 23264.703 674 0 -4565.8054 0 -4565.8054 -3755.6253 22905.955 Loop time of 77.4185 on 1 procs for 420 steps with 1364 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4563.8211199 -4565.8054195 -4565.8054195 Force two-norm initial, final = 286.692 0.00283881 Force max component initial, final = 251.719 0.00124977 Final line search alpha, max atom move = 0.000976562 1.22048e-06 Iterations, force evaluations = 420 949 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.17 | 77.17 | 77.17 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.066382 | 0.066382 | 0.066382 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1822 | | | 0.24 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16059 ave 16059 max 16059 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: 73612 ave 73612 max 73612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73612 Ave neighs/atom = 53.9677 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 17 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (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) = 12.23 | 12.23 | 12.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4565.8054 0 -4565.8054 -3755.6253 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1364 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: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16129 ave 16129 max 16129 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: 73844 ave 73844 max 73844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73844 Ave neighs/atom = 54.1378 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 -4565.8054 -4565.8054 52.653157 106.97498 4.0666968 -3755.6253 -3755.6253 -0.061527883 -11266.727 -0.087425729 2.3328597 734.23166 Loop time of 0 on 1 procs for 0 steps with 1364 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 | | 0 | | | 0.00 Nlocal: 1364 ave 1364 max 1364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16129 ave 16129 max 16129 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36922 ave 36922 max 36922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73844 ave 73844 max 73844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73844 Ave neighs/atom = 54.1378 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_017.4923/numatoms.out 1364 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4565.80541950151-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4565.80541950151-1364*${isolated_atom_energy} variable adjusted_pe_metal equal -4565.80541950151-1364*0 print "${adjusted_pe_metal} eV" file output/dump_017.4923/energy.out -4565.80541950151 eV print "${mindist_metal} Angstroms" file output/dump_017.4923/mindistance.out 2.33285965030166 Angstroms write_dump all cfg output/dump_017.4923/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_017.4923/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:59