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 4.050000071525574*${_u_distance} variable lattice_constant_converted equal 4.050000071525574*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 57.56131615095458*${_u_distance} variable xmax_converted equal 57.56131615095458*1 variable ymin_converted equal -57.565366151026105*${_u_distance} variable ymin_converted equal -57.565366151026105*1 variable ymax_converted equal 57.565366151026105*${_u_distance} variable ymax_converted equal 57.565366151026105*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000071525574*${_u_distance} variable zmax_converted equal 4.050000071525574*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000007152557 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 57.5613161509546 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.5613161509546 -57.5653661510261 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 57.5613161509546 -57.5653661510261 57.5653661510261 ${zmin_converted} ${zmax_converted} units box region whole block 0 57.5613161509546 -57.5653661510261 57.5653661510261 0 ${zmax_converted} units box region whole block 0 57.5613161509546 -57.5653661510261 57.5653661510261 0 4.05000007152557 units box create_box 2 whole Created orthogonal box = (0 -57.5654 0) to (57.5613 57.5654 4.05) 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 57.5653661510261 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 11 -9 0 orient y 9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69914 5.69914 4.05 create_atoms 1 region upper Created 809 atoms create_atoms CPU = 0.000389099 secs group upper type 1 809 atoms in group upper mass 1 26.981538*${_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 -57.5653661510261 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 11 9 0 orient y -9 11 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.69914 5.69914 4.05 create_atoms 2 region lower Created 809 atoms create_atoms CPU = 0.000219107 secs group lower type 2 809 atoms in group lower displace_atoms lower move -6.395701681598353 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005 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*4.05000007152557 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500003576279 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 14 28 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 8.28721 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 14 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5325.3673 0 -5325.3673 -1821.6593 330 0 -5344.317 0 -5344.317 -6752.5231 Loop time of 3.38305 on 1 procs for 330 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 = -5325.36727996 -5344.31702216 -5344.31702216 Force two-norm initial, final = 13.7531 3.69725e-06 Force max component initial, final = 2.26931 1.50513e-06 Final line search alpha, max atom move = 1 1.50513e-06 Iterations, force evaluations = 330 641 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3074 | 3.3074 | 3.3074 | 0.0 | 97.76 Neigh | 0.014761 | 0.014761 | 0.014761 | 0.0 | 0.44 Comm | 0.037555 | 0.037555 | 0.037555 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02336 | | | 0.69 Nlocal: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10120 ave 10120 max 10120 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: 222102 ave 222102 max 222102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222102 Ave neighs/atom = 139.249 Neighbor list builds = 3 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) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 330 0 -5344.317 0 -5344.317 -6752.5231 26839.66 1330 0 -5344.6705 0 -5344.6705 -1377.1533 26654.551 Loop time of 10.0446 on 1 procs for 1000 steps with 1595 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 = -5344.31702216 -5344.67047693 -5344.67047697 Force two-norm initial, final = 144.296 0.0215599 Force max component initial, final = 103.151 0.0198123 Final line search alpha, max atom move = 0.0441793 0.000875294 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.5718 | 9.5718 | 9.5718 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10342 | 0.10342 | 0.10342 | 0.0 | 1.03 Output | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3694 | | | 3.68 Nlocal: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10120 ave 10120 max 10120 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: 222092 ave 222092 max 222092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222092 Ave neighs/atom = 139.243 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 -4.3766955338e-11 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 14 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5344.6705 0 -5344.6705 -1377.1533 Loop time of 1.19209e-06 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 | | 1.192e-06 | | |100.00 Nlocal: 1595 ave 1595 max 1595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10125 ave 10125 max 10125 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: 222170 ave 222170 max 222170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222170 Ave neighs/atom = 139.292 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) = 5.682 | 5.682 | 5.682 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 -5344.6705 -5344.6705 57.36348 115.13073 4.0359392 -1377.1533 -1377.1533 1.1868055 -4132.2509 -0.39569378 2.5092268 688.34421 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: 10125 ave 10125 max 10125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111085 ave 111085 max 111085 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 222170 ave 222170 max 222170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222170 Ave neighs/atom = 139.292 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -5344.67047696518-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5344.67047696518-1595*${isolated_atom_energy} variable adjusted_pe_metal equal -5344.67047696518-1595*-4.3766955338e-11 print "${adjusted_pe_metal} eV" file output/dump_078.5788/energy.out -5344.67047689537 eV print "${mindist_metal} Angstroms" file output/dump_078.5788/mindistance.out 2.50922683297997 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: 0:00:13