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 58.22011549833317*${_u_distance} variable xmax_converted equal 58.22011549833317*1 variable ymin_converted equal -58.2241817675819*${_u_distance} variable ymin_converted equal -58.2241817675819*1 variable ymax_converted equal 58.2241817675819*${_u_distance} variable ymax_converted equal 58.2241817675819*1 variable zmin_converted equal 0.0*${_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 58.2201154983332 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 58.2201154983332 -58.2241817675819 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 58.2201154983332 -58.2241817675819 58.2241817675819 ${zmin_converted} ${zmax_converted} units box region whole block 0 58.2201154983332 -58.2241817675819 58.2241817675819 0 ${zmax_converted} units box region whole block 0 58.2201154983332 -58.2241817675819 58.2241817675819 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -58.2242 0) to (58.2201 58.2242 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 58.2241817675819 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 14 -3 0 orient y 3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.82801 4.82801 4.06627 create_atoms 1 region upper Created 822 atoms create_atoms CPU = 0.000232935 secs group upper type 1 822 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.44301947847436 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -58.2241817675819 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 14 3 0 orient y -3 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.82801 4.82801 4.06627 create_atoms 2 region lower Created 822 atoms create_atoms CPU = 0.000128984 secs group lower type 2 822 atoms in group lower displace_atoms lower move -6.44301947847436 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 38 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 = 1620 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 38 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) = 14.06 | 14.06 | 14.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5399.9795 0 -5399.9795 -9794.8051 294 0 -5420.6638 0 -5420.6638 -13915.02 Loop time of 56.3239 on 1 procs for 294 steps with 1620 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 = -5399.97945164 -5420.66383927 -5420.66383927 Force two-norm initial, final = 8.90192 3.3094e-05 Force max component initial, final = 1.30133 2.45514e-06 Final line search alpha, max atom move = 1 2.45514e-06 Iterations, force evaluations = 294 574 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.227 | 56.227 | 56.227 | 0.0 | 99.83 Neigh | 0.030392 | 0.030392 | 0.030392 | 0.0 | 0.05 Comm | 0.047868 | 0.047868 | 0.047868 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0184 | | | 0.03 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18230 ave 18230 max 18230 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: 87412 ave 87412 max 87412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87412 Ave neighs/atom = 53.958 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) = 14.09 | 14.09 | 14.09 Mbytes Step Temp E_pair E_mol TotEng Press Volume 294 0 -5420.6638 0 -5420.6638 -13915.02 27567.83 392 0 -5422.5802 0 -5422.5802 -3164.0707 27183.2 Loop time of 20.8904 on 1 procs for 98 steps with 1620 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 = -5420.66383927 -5422.58019161 -5422.58019161 Force two-norm initial, final = 306.815 0.0262498 Force max component initial, final = 269.3 0.00763441 Final line search alpha, max atom move = 1.22783e-05 9.37375e-08 Iterations, force evaluations = 98 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.827 | 20.827 | 20.827 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016866 | 0.016866 | 0.016866 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04638 | | | 0.22 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18218 ave 18218 max 18218 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: 87348 ave 87348 max 87348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87348 Ave neighs/atom = 53.9185 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 = 19 38 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) = 12.72 | 12.72 | 12.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5422.5802 0 -5422.5802 -3164.0707 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1620 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: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18302 ave 18302 max 18302 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: 87492 ave 87492 max 87492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87492 Ave neighs/atom = 54.0074 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) = 12.72 | 12.72 | 12.72 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 -5422.5802 -5422.5802 57.405075 116.44836 4.0664637 -3164.0707 -3164.0707 0.28888786 -9492.4224 -0.078514265 2.2806566 1052.6257 Loop time of 1.62125e-05 on 1 procs for 0 steps with 1620 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 | | 1.621e-05 | | |100.00 Nlocal: 1620 ave 1620 max 1620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18302 ave 18302 max 18302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43746 ave 43746 max 43746 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87492 ave 87492 max 87492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87492 Ave neighs/atom = 54.0074 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_024.1895/numatoms.out 1620 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.58019160552-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.58019160552-1620*${isolated_atom_energy} variable adjusted_pe_metal equal -5422.58019160552-1620*0 print "${adjusted_pe_metal} eV" file output/dump_024.1895/energy.out -5422.58019160552 eV print "${mindist_metal} Angstroms" file output/dump_024.1895/mindistance.out 2.28065659391799 Angstroms write_dump all cfg output/dump_024.1895/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_024.1895/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:17