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 3.869337007403374*${_u_distance} variable lattice_constant_converted equal 3.869337007403374*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 54.993611566489996*${_u_distance} variable xmax_converted equal 54.993611566489996*1 variable ymin_converted equal -54.9974809034974*${_u_distance} variable ymin_converted equal -54.9974809034974*1 variable ymax_converted equal 54.9974809034974*${_u_distance} variable ymax_converted equal 54.9974809034974*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.869337007403374*${_u_distance} variable zmax_converted equal 3.869337007403374*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.86933700740337 Lattice spacing in x,y,z = 3.86934 3.86934 3.86934 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 54.99361156649 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.99361156649 -54.9974809034974 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 54.99361156649 -54.9974809034974 54.9974809034974 ${zmin_converted} ${zmax_converted} units box region whole block 0 54.99361156649 -54.9974809034974 54.9974809034974 0 ${zmax_converted} units box region whole block 0 54.99361156649 -54.9974809034974 54.9974809034974 0 3.86933700740337 units box create_box 2 whole Created orthogonal box = (0 -54.9975 0) to (54.9936 54.9975 3.86934) 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 54.9974809034974 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 lattice fcc 3.86933700740337 orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.44491 5.44491 3.86934 create_atoms 1 region upper Created 809 atoms create_atoms CPU = 0.000356197 secs group upper type 1 809 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.395701681598353 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -54.9974809034974 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 lattice fcc 3.86933700740337 orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.44491 5.44491 3.86934 create_atoms 2 region lower Created 809 atoms create_atoms CPU = 0.000225782 secs group lower type 2 809 atoms in group lower displace_atoms lower move -6.395701681598353 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_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*3.86933700740337 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.93466850370169 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 14 27 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 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 23 atoms, new total = 1595 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 14 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5055.1477 0 -5055.1477 32.278589 315 0 -5098.0525 0 -5098.0525 -13469.633 Loop time of 3.62355 on 1 procs for 315 steps with 1595 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5055.14774684 -5098.05247319 -5098.05247319 Force two-norm initial, final = 56.1441 5.18088e-05 Force max component initial, final = 14.1946 1.38017e-05 Final line search alpha, max atom move = 1 1.38017e-05 Iterations, force evaluations = 315 607 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.536 | 3.536 | 3.536 | 0.0 | 97.58 Neigh | 0.031434 | 0.031434 | 0.031434 | 0.0 | 0.87 Comm | 0.034891 | 0.034891 | 0.034891 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0212 | | | 0.59 Nlocal: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10300 ave 10300 max 10300 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: 233198 ave 233198 max 233198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233198 Ave neighs/atom = 146.206 Neighbor list builds = 5 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) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 315 0 -5098.0525 0 -5098.0525 -13469.633 23405.698 1315 0 -5098.6836 0 -5098.6836 -2946.7111 23233.206 Loop time of 11.9006 on 1 procs for 1000 steps with 1595 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5098.05247319 -5098.68356966 -5098.68356967 Force two-norm initial, final = 237.432 0.0157451 Force max component initial, final = 173.182 0.0151663 Final line search alpha, max atom move = 0.4862 0.00737388 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.431 | 11.431 | 11.431 | 0.0 | 96.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1038 | 0.1038 | 0.1038 | 0.0 | 0.87 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3656 | | | 3.07 Nlocal: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10285 ave 10285 max 10285 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: 231092 ave 231092 max 231092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231092 Ave neighs/atom = 144.885 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 14 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5098.6836 0 -5098.6836 -2946.7111 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1595 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: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10285 ave 10285 max 10285 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: 248042 ave 248042 max 248042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248042 Ave neighs/atom = 155.512 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) = 5.687 | 5.687 | 5.687 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 -5098.6836 -5098.6836 54.858344 109.99496 3.8502919 -2946.7111 -2946.7111 -0.16985137 -8838.9228 -1.040732 2.416698 407.80512 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1595 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: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10285 ave 10285 max 10285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124021 ave 124021 max 124021 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248042 ave 248042 max 248042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248042 Ave neighs/atom = 155.512 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_078.5788/numatoms.out 1595 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5098.68356966537-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5098.68356966537-1595*${isolated_atom_energy} variable adjusted_pe_metal equal -5098.68356966537-1595*0 print "${adjusted_pe_metal} eV" file output/dump_078.5788/energy.out -5098.68356966537 eV print "${mindist_metal} Angstroms" file output/dump_078.5788/mindistance.out 2.41669797311572 Angstroms write_dump all cfg output/dump_078.5788/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_078.5788/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15