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 45.462272274819135*${_u_distance} variable xmax_converted equal 45.462272274819135*1 variable ymin_converted equal -45.46633854406786*${_u_distance} variable ymin_converted equal -45.46633854406786*1 variable ymax_converted equal 45.46633854406786*${_u_distance} variable ymax_converted equal 45.46633854406786*1 variable zmin_converted equal 0.0*${_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 45.4622722748191 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.4622722748191 -45.4663385440679 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 45.4622722748191 -45.4663385440679 45.4663385440679 ${zmin_converted} ${zmax_converted} units box region whole block 0 45.4622722748191 -45.4663385440679 45.4663385440679 0 ${zmax_converted} units box region whole block 0 45.4622722748191 -45.4663385440679 45.4663385440679 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -45.4663 0) to (45.4623 45.4663 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 45.4663385440679 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 11 -2 0 orient y 2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.72808 4.72808 4.06627 create_atoms 1 region upper Created 502 atoms create_atoms CPU = 0.000210047 secs group upper type 1 502 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.031152949374526 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -45.4663385440679 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 11 2 0 orient y -2 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.72808 4.72808 4.06627 create_atoms 2 region lower Created 502 atoms create_atoms CPU = 8.01086e-05 secs group lower type 2 502 atoms in group lower displace_atoms lower move -5.031152949374526 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 15 30 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 20 atoms, new total = 984 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 = 15 30 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) = 8.855 | 8.855 | 8.855 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3275.5625 0 -3275.5625 -11090.763 181 0 -3289.8109 0 -3289.8109 -16427.231 Loop time of 53.1585 on 1 procs for 181 steps with 984 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 = -3275.56253194 -3289.81086746 -3289.81086746 Force two-norm initial, final = 7.42685 0.00794519 Force max component initial, final = 1.55323 0.00250639 Final line search alpha, max atom move = 0.000244141 6.11913e-07 Iterations, force evaluations = 181 898 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.07 | 53.07 | 53.07 | 0.0 | 99.83 Neigh | 0.020879 | 0.020879 | 0.020879 | 0.0 | 0.04 Comm | 0.052576 | 0.052576 | 0.052576 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01525 | | | 0.03 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12764 ave 12764 max 12764 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: 53052 ave 53052 max 53052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53052 Ave neighs/atom = 53.9146 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) = 8.868 | 8.868 | 8.868 Mbytes Step Temp E_pair E_mol TotEng Press Volume 181 0 -3289.8109 0 -3289.8109 -16427.231 16809.982 366 0 -3291.3692 0 -3291.3692 -3712.1164 16535.731 Loop time of 22.9095 on 1 procs for 185 steps with 984 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 = -3289.81086746 -3291.36920089 -3291.36920089 Force two-norm initial, final = 219.379 0.173189 Force max component initial, final = 189.757 0.164181 Final line search alpha, max atom move = 2.39725e-07 3.93584e-08 Iterations, force evaluations = 185 386 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.83 | 22.83 | 22.83 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022011 | 0.022011 | 0.022011 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05794 | | | 0.25 Nlocal: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12764 ave 12764 max 12764 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: 53056 ave 53056 max 53056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53056 Ave neighs/atom = 53.9187 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 = 15 30 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) = 8.376 | 8.376 | 8.376 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3291.3692 0 -3291.3692 -3712.1164 Loop time of 9.53674e-07 on 1 procs for 0 steps with 984 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: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12834 ave 12834 max 12834 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: 53296 ave 53296 max 53296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53296 Ave neighs/atom = 54.1626 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) = 8.376 | 8.376 | 8.376 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 -3291.3692 -3291.3692 44.743244 90.932677 4.0642082 -3712.1164 -3712.1164 -15.656211 -11125.278 4.5852727 2.3769869 757.71343 Loop time of 9.53674e-07 on 1 procs for 0 steps with 984 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: 984 ave 984 max 984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12834 ave 12834 max 12834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26648 ave 26648 max 26648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53296 ave 53296 max 53296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53296 Ave neighs/atom = 54.1626 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_020.6097/numatoms.out 984 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3291.36920089219-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3291.36920089219-984*${isolated_atom_energy} variable adjusted_pe_metal equal -3291.36920089219-984*0 print "${adjusted_pe_metal} eV" file output/dump_020.6097/energy.out -3291.36920089219 eV print "${mindist_metal} Angstroms" file output/dump_020.6097/mindistance.out 2.37698689534437 Angstroms write_dump all cfg output/dump_020.6097/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_020.6097/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:16