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 37.48915011393372*${_u_distance} variable xmax_converted equal 37.48915011393372*1 variable ymin_converted equal -74.98236649711616*${_u_distance} variable ymin_converted equal -74.98236649711616*1 variable ymax_converted equal 74.98236649711616*${_u_distance} variable ymax_converted equal 74.98236649711616*1 variable zmin_converted equal 0.0*${_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 37.4891501139337 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.4891501139337 -74.9823664971162 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 37.4891501139337 -74.9823664971162 74.9823664971162 ${zmin_converted} ${zmax_converted} units box region whole block 0 37.4891501139337 -74.9823664971162 74.9823664971162 0 ${zmax_converted} units box region whole block 0 37.4891501139337 -74.9823664971162 74.9823664971162 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -74.9824 0) to (37.4892 74.9824 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 74.9823664971162 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 9 -2 0 orient y 2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.85154 4.85154 4.06627 create_atoms 1 region upper Created 682 atoms create_atoms CPU = 0.000217915 secs group upper type 1 682 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.148795005781799 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -74.9823664971162 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 9 2 0 orient y -2 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.85154 4.85154 4.06627 create_atoms 2 region lower Created 682 atoms create_atoms CPU = 0.000108957 secs group lower type 2 682 atoms in group lower displace_atoms lower move -4.148795005781799 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 13 49 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 12 atoms, new total = 1352 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 = 13 49 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) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4514.9586 0 -4514.9586 -8277.5834 254 0 -4529.3122 0 -4529.3122 -9858.4783 Loop time of 40.6542 on 1 procs for 254 steps with 1352 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 = -4514.95862865 -4529.31216872 -4529.31216872 Force two-norm initial, final = 10.1944 2.59369e-06 Force max component initial, final = 2.11534 1.45042e-07 Final line search alpha, max atom move = 1 1.45042e-07 Iterations, force evaluations = 254 493 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.574 | 40.574 | 40.574 | 0.0 | 99.80 Neigh | 0.026659 | 0.026659 | 0.026659 | 0.0 | 0.07 Comm | 0.03997 | 0.03997 | 0.03997 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01379 | | | 0.03 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17163 ave 17163 max 17163 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: 72956 ave 72956 max 72956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72956 Ave neighs/atom = 53.9615 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) = 13.65 | 13.65 | 13.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 254 0 -4529.3122 0 -4529.3122 -9858.4783 22860.771 731 0 -4530.3461 0 -4530.3461 -2170.016 22627.854 Loop time of 80.8764 on 1 procs for 477 steps with 1352 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 = -4529.31216872 -4530.34608856 -4530.34608856 Force two-norm initial, final = 190.046 0.0256533 Force max component initial, final = 178.071 0.0183058 Final line search alpha, max atom move = 9.45528e-06 1.73086e-07 Iterations, force evaluations = 477 980 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 80.604 | 80.604 | 80.604 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.073529 | 0.073529 | 0.073529 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1987 | | | 0.25 Nlocal: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17233 ave 17233 max 17233 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: 73000 ave 73000 max 73000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73000 Ave neighs/atom = 53.9941 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 = 12 49 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) = 12.27 | 12.27 | 12.27 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4530.3461 0 -4530.3461 -2170.016 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17233 ave 17233 max 17233 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: 73056 ave 73056 max 73056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73056 Ave neighs/atom = 54.0355 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) = 12.27 | 12.27 | 12.27 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 -4530.3461 -4530.3461 37.034588 149.96473 4.0742409 -2170.016 -2170.016 -1.1907975 -6507.5584 -1.2986915 2.3172232 652.54484 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1352 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: 1352 ave 1352 max 1352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17233 ave 17233 max 17233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36528 ave 36528 max 36528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73056 ave 73056 max 73056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73056 Ave neighs/atom = 54.0355 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_025.0576/numatoms.out 1352 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4530.34608855589-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4530.34608855589-1352*${isolated_atom_energy} variable adjusted_pe_metal equal -4530.34608855589-1352*0 print "${adjusted_pe_metal} eV" file output/dump_025.0576/energy.out -4530.34608855589 eV print "${mindist_metal} Angstroms" file output/dump_025.0576/mindistance.out 2.31722319327877 Angstroms write_dump all cfg output/dump_025.0576/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_025.0576/success.out This indicates that LAMMPS ran successfully Total wall time: 0:02:02