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 4.210718545317654*${_u_distance} variable lattice_constant_converted equal 4.210718545317654*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 63.30097985767153*${_u_distance} variable xmax_converted equal 63.30097985767153*1 variable ymin_converted equal -63.305190576216845*${_u_distance} variable ymin_converted equal -63.305190576216845*1 variable ymax_converted equal 63.305190576216845*${_u_distance} variable ymax_converted equal 63.305190576216845*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210718545317654*${_u_distance} variable zmax_converted equal 4.210718545317654*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21071854531765 Lattice spacing in x,y,z = 4.21072 4.21072 4.21072 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 63.3009798576715 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.3009798576715 -63.3051905762168 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.3009798576715 -63.3051905762168 63.3051905762168 ${zmin_converted} ${zmax_converted} units box region whole block 0 63.3009798576715 -63.3051905762168 63.3051905762168 0 ${zmax_converted} units box region whole block 0 63.3009798576715 -63.3051905762168 63.3051905762168 0 4.21071854531765 units box create_box 2 whole Created orthogonal box = (0 -63.3052 0) to (63.301 63.3052 4.21072) 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 63.3051905762168 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.48149 4.48149 4.21072 create_atoms 1 region upper Created 906 atoms create_atoms CPU = 0.000242949 secs group upper type 1 906 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.764983370267808 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -63.3051905762168 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 lattice fcc 4.21071854531765 orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.48149 4.48149 4.21072 create_atoms 2 region lower Created 906 atoms create_atoms CPU = 0.000118971 secs group lower type 2 906 atoms in group lower displace_atoms lower move -6.764983370267808 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000 pair_coeff * * Al Al 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*4.21071854531765 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535927265882 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 15 29 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1784 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.975 | 5.975 | 5.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6634.1139 0 -6634.1139 -980.72753 284 0 -6643.2113 0 -6643.2113 -3220.9768 Loop time of 4.04471 on 1 procs for 284 steps with 1784 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6634.11385444 -6643.21129008 -6643.21129008 Force two-norm initial, final = 9.40893 1.65866e-06 Force max component initial, final = 2.63352 2.75889e-07 Final line search alpha, max atom move = 1 2.75889e-07 Iterations, force evaluations = 284 555 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9771 | 3.9771 | 3.9771 | 0.0 | 98.33 Neigh | 0.0073671 | 0.0073671 | 0.0073671 | 0.0 | 0.18 Comm | 0.037458 | 0.037458 | 0.037458 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02279 | | | 0.56 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11346 ave 11346 max 11346 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: 303916 ave 303916 max 303916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303916 Ave neighs/atom = 170.357 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) = 5.985 | 5.985 | 5.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 284 0 -6643.2113 0 -6643.2113 -3220.9768 33747.061 1284 0 -6643.3974 0 -6643.3974 -779.14505 33531.926 Loop time of 14.1674 on 1 procs for 1000 steps with 1784 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -6643.21129008 -6643.39735558 -6643.3973556 Force two-norm initial, final = 80.8256 0.00890566 Force max component initial, final = 58.9786 0.00716143 Final line search alpha, max atom move = 0.0689127 0.000493514 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.583 | 13.583 | 13.583 | 0.0 | 95.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13239 | 0.13239 | 0.13239 | 0.0 | 0.93 Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4518 | | | 3.19 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12536 ave 12536 max 12536 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: 303636 ave 303636 max 303636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303636 Ave neighs/atom = 170.2 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 -0.09604918 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (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) = 6.123 | 6.123 | 6.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6643.3974 0 -6643.3974 -779.14505 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12585 ave 12585 max 12585 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: 305556 ave 305556 max 305556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305556 Ave neighs/atom = 171.276 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) = 6.123 | 6.123 | 6.123 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 -6643.3974 -6643.3974 63.119857 126.61038 4.1958811 -779.14505 -779.14505 -0.34119864 -2337.1208 0.026844754 2.7425187 1208.5861 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12585 ave 12585 max 12585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152778 ave 152778 max 152778 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 305556 ave 305556 max 305556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305556 Ave neighs/atom = 171.276 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_007.6281/numatoms.out 1784 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6643.39735560242-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6643.39735560242-1784*${isolated_atom_energy} variable adjusted_pe_metal equal -6643.39735560242-1784*-0.09604918 print "${adjusted_pe_metal} eV" file output/dump_007.6281/energy.out -6472.04561848242 eV print "${mindist_metal} Angstroms" file output/dump_007.6281/mindistance.out 2.74251870851174 Angstroms write_dump all cfg output/dump_007.6281/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_007.6281/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18