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 56.63657693580141*${_u_distance} variable xmax_converted equal 56.63657693580141*1 variable ymin_converted equal -56.64064320505013*${_u_distance} variable ymin_converted equal -56.64064320505013*1 variable ymax_converted equal 56.64064320505013*${_u_distance} variable ymax_converted equal 56.64064320505013*1 variable zmin_converted equal 0.0*${_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 56.6365769358014 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.6365769358014 -56.6406432050501 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 56.6365769358014 -56.6406432050501 56.6406432050501 ${zmin_converted} ${zmax_converted} units box region whole block 0 56.6365769358014 -56.6406432050501 56.6406432050501 0 ${zmax_converted} units box region whole block 0 56.6365769358014 -56.6406432050501 56.6406432050501 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -56.6406 0) to (56.6366 56.6406 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 56.6406432050501 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 13 -5 0 orient y 5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.25494 5.25494 4.06627 create_atoms 1 region upper Created 778 atoms create_atoms CPU = 0.000236988 secs group upper type 1 778 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.267774724732854 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -56.6406432050501 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 13 5 0 orient y -5 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.25494 5.25494 4.06627 create_atoms 2 region lower Created 778 atoms create_atoms CPU = 0.000131845 secs group lower type 2 778 atoms in group lower displace_atoms lower move -6.267774724732854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 19 37 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 26 atoms, new total = 1530 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 = 19 37 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) = 14.03 | 14.03 | 14.03 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5096.5103 0 -5096.5103 -10067.864 173 0 -5117.5017 0 -5117.5017 -15001.571 Loop time of 33.8477 on 1 procs for 173 steps with 1530 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 = -5096.51025487 -5117.50165219 -5117.50165219 Force two-norm initial, final = 9.52138 0.00667521 Force max component initial, final = 1.68643 0.00282527 Final line search alpha, max atom move = 0.5 0.00141263 Iterations, force evaluations = 173 368 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.779 | 33.779 | 33.779 | 0.0 | 99.80 Neigh | 0.028178 | 0.028178 | 0.028178 | 0.0 | 0.08 Comm | 0.029196 | 0.029196 | 0.029196 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01087 | | | 0.03 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17433 ave 17433 max 17433 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: 82468 ave 82468 max 82468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82468 Ave neighs/atom = 53.9007 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) = 14.03 | 14.03 | 14.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 173 0 -5117.5017 0 -5117.5017 -15001.571 26088.632 1076 0 -5119.362 0 -5119.362 -3783.0915 25705.38 Loop time of 167.028 on 1 procs for 903 steps with 1530 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 = -5117.50165219 -5119.3619605 -5119.3619605 Force two-norm initial, final = 301.472 0.0131094 Force max component initial, final = 256.794 0.00946381 Final line search alpha, max atom move = 6.89645e-05 6.52667e-07 Iterations, force evaluations = 903 1808 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 166.48 | 166.48 | 166.48 | 0.0 | 99.67 Neigh | 0.027254 | 0.027254 | 0.027254 | 0.0 | 0.02 Comm | 0.13824 | 0.13824 | 0.13824 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3798 | | | 0.23 Nlocal: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17503 ave 17503 max 17503 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: 82708 ave 82708 max 82708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82708 Ave neighs/atom = 54.0575 Neighbor list builds = 1 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 = 19 37 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) = 12.69 | 12.69 | 12.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5119.362 0 -5119.362 -3783.0915 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17503 ave 17503 max 17503 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: 82676 ave 82676 max 82676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82676 Ave neighs/atom = 54.0366 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) = 12.69 | 12.69 | 12.69 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 -5119.362 -5119.362 55.861422 113.28129 4.0621306 -3783.0915 -3783.0915 0.36838547 -11350.232 0.58926402 2.2163853 957.88872 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1530 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: 1530 ave 1530 max 1530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17503 ave 17503 max 17503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41338 ave 41338 max 41338 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82676 ave 82676 max 82676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82676 Ave neighs/atom = 54.0366 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_042.0750/numatoms.out 1530 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5119.36196050498-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5119.36196050498-1530*${isolated_atom_energy} variable adjusted_pe_metal equal -5119.36196050498-1530*0 print "${adjusted_pe_metal} eV" file output/dump_042.0750/energy.out -5119.36196050498 eV print "${mindist_metal} Angstroms" file output/dump_042.0750/mindistance.out 2.21638532363448 Angstroms write_dump all cfg output/dump_042.0750/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_042.0750/success.out This indicates that LAMMPS ran successfully Total wall time: 0:03:21