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 48.76845890539076*${_u_distance} variable xmax_converted equal 48.76845890539076*1 variable ymin_converted equal -48.77250890546228*${_u_distance} variable ymin_converted equal -48.77250890546228*1 variable ymax_converted equal 48.77250890546228*${_u_distance} variable ymax_converted equal 48.77250890546228*1 variable zmin_converted equal 0.0*${_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 48.7684589053908 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684589053908 -48.7725089054623 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684589053908 -48.7725089054623 48.7725089054623 ${zmin_converted} ${zmax_converted} units box region whole block 0 48.7684589053908 -48.7725089054623 48.7725089054623 0 ${zmax_converted} units box region whole block 0 48.7684589053908 -48.7725089054623 48.7725089054623 0 4.05000007152557 units box create_box 2 whole Created orthogonal box = (0 -48.7725 0) to (48.7685 48.7725 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 48.7725089054623 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -1 0 orient y 1 12 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 12 -1 0 orient y 1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37234 4.37234 4.05 create_atoms 1 region upper Created 582 atoms create_atoms CPU = 0.000197887 secs group upper type 1 582 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.418717560456534 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -48.7725089054623 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 1 0 orient y -1 12 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 12 1 0 orient y -1 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.37234 4.37234 4.05 create_atoms 2 region lower Created 582 atoms create_atoms CPU = 7.82013e-05 secs group lower type 2 582 atoms in group lower displace_atoms lower move -5.418717560456534 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 12 24 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 22 atoms, new total = 1142 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 = 12 24 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3812.7125 0 -3812.7125 -1816.0551 197 0 -3825.6849 0 -3825.6849 -9278.1566 Loop time of 1.43099 on 1 procs for 197 steps with 1142 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 = -3812.712503 -3825.68488531 -3825.68488531 Force two-norm initial, final = 10.2619 4.26548e-07 Force max component initial, final = 2.80559 6.8684e-08 Final line search alpha, max atom move = 1 6.8684e-08 Iterations, force evaluations = 197 386 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4 | 1.4 | 1.4 | 0.0 | 97.84 Neigh | 0.0031369 | 0.0031369 | 0.0031369 | 0.0 | 0.22 Comm | 0.017402 | 0.017402 | 0.017402 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01043 | | | 0.73 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7819 ave 7819 max 7819 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: 159216 ave 159216 max 159216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159216 Ave neighs/atom = 139.419 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) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press Volume 197 0 -3825.6849 0 -3825.6849 -9278.1566 19266.337 1197 0 -3826.0738 0 -3826.0738 -2552.092 19100.738 Loop time of 7.34277 on 1 procs for 1000 steps with 1142 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3825.68488531 -3826.07384787 -3826.07384793 Force two-norm initial, final = 127.241 0.0252384 Force max component initial, final = 90.507 0.0221583 Final line search alpha, max atom move = 0.043741 0.000969228 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9801 | 6.9801 | 6.9801 | 0.0 | 95.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080924 | 0.080924 | 0.080924 | 0.0 | 1.10 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2818 | | | 3.84 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7825 ave 7825 max 7825 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: 159244 ave 159244 max 159244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159244 Ave neighs/atom = 139.443 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 = 12 24 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) = 5.182 | 5.182 | 5.182 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3826.0738 0 -3826.0738 -2552.092 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1142 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: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827 ave 7827 max 7827 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: 159396 ave 159396 max 159396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159396 Ave neighs/atom = 139.576 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) = 5.182 | 5.182 | 5.182 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 -3826.0738 -3826.0738 48.559438 97.545018 4.0324724 -2552.092 -2552.092 -0.68161106 -7657.4449 1.8506047 2.5882509 350.90024 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1142 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 | | 2.146e-06 | | |100.00 Nlocal: 1142 ave 1142 max 1142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827 ave 7827 max 7827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79698 ave 79698 max 79698 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159396 ave 159396 max 159396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159396 Ave neighs/atom = 139.576 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_009.5273/numatoms.out 1142 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.07384792614-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.07384792614-1142*${isolated_atom_energy} variable adjusted_pe_metal equal -3826.07384792614-1142*-4.3766955338e-11 print "${adjusted_pe_metal} eV" file output/dump_009.5273/energy.out -3826.07384787616 eV print "${mindist_metal} Angstroms" file output/dump_009.5273/mindistance.out 2.58825087809603 Angstroms write_dump all cfg output/dump_009.5273/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_009.5273/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:08