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 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 29.657115648638918*${_u_distance} variable xmax_converted equal 29.657115648638918*1 variable ymin_converted equal -59.31830501540843*${_u_distance} variable ymin_converted equal -59.31830501540843*1 variable ymax_converted equal 59.31830501540843*${_u_distance} variable ymax_converted equal 59.31830501540843*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 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 29.6571156486389 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.6571156486389 -59.3183050154084 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.6571156486389 -59.3183050154084 59.3183050154084 ${zmin_converted} ${zmax_converted} units box region whole block 0 29.6571156486389 -59.3183050154084 59.3183050154084 0 ${zmax_converted} units box region whole block 0 29.6571156486389 -59.3183050154084 59.3183050154084 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -59.3183 0) to (29.6571 59.3183 4.07372) 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 59.3183050154084 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.03611 5.03611 4.07372 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.00018692 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 3.276049450176233 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.3183050154084 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.03611 5.03611 4.07372 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 7.51019e-05 secs group lower type 2 426 atoms in group lower displace_atoms lower move -3.276049450176233 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 26 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 834 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2539.1529 0 -2539.1529 15.575829 284 0 -2550.497 0 -2550.497 -4509.8423 Loop time of 2.64101 on 1 procs for 284 steps with 834 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 = -2539.15293287 -2550.49699196 -2550.49699196 Force two-norm initial, final = 14.3451 8.37607e-06 Force max component initial, final = 4.89518 1.05709e-06 Final line search alpha, max atom move = 1 1.05709e-06 Iterations, force evaluations = 284 552 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5968 | 2.5968 | 2.5968 | 0.0 | 98.33 Neigh | 0.0070181 | 0.0070181 | 0.0070181 | 0.0 | 0.27 Comm | 0.025486 | 0.025486 | 0.025486 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01166 | | | 0.44 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7824 ave 7824 max 7824 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: 165116 ave 165116 max 165116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165116 Ave neighs/atom = 197.981 Neighbor list builds = 2 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) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 284 0 -2550.497 0 -2550.497 -4509.8423 14333.05 1284 0 -2550.5825 0 -2550.5825 -1747.1669 14249.319 Loop time of 10.0708 on 1 procs for 1000 steps with 834 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 = -2550.49699196 -2550.58249178 -2550.58249178 Force two-norm initial, final = 40.1292 0.00201502 Force max component initial, final = 30.8736 0.00166918 Final line search alpha, max atom move = 1 0.00166918 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7039 | 9.7039 | 9.7039 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.088842 | 0.088842 | 0.088842 | 0.0 | 0.88 Output | 3.2187e-05 | 3.2187e-05 | 3.2187e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.278 | | | 2.76 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8574 ave 8574 max 8574 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: 165296 ave 165296 max 165296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165296 Ave neighs/atom = 198.197 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 0.143095413925774 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.151 | 5.151 | 5.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2550.5825 0 -2550.5825 -1747.1669 Loop time of 1.19209e-06 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8586 ave 8586 max 8586 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: 165360 ave 165360 max 165360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165360 Ave neighs/atom = 198.273 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) = 5.151 | 5.151 | 5.151 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 -2550.5825 -2550.5825 29.599269 118.63661 4.0578353 -1747.1669 -1747.1669 0.037758246 -5241.7255 0.18694908 2.5633217 553.53007 Loop time of 9.53674e-07 on 1 procs for 0 steps with 834 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: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8586 ave 8586 max 8586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82680 ave 82680 max 82680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 165360 ave 165360 max 165360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165360 Ave neighs/atom = 198.273 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_031.8908/numatoms.out 834 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2550.58249178469-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2550.58249178469-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2550.58249178469-834*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_031.8908/energy.out -2669.92406699879 eV print "${mindist_metal} Angstroms" file output/dump_031.8908/mindistance.out 2.56332167108089 Angstroms write_dump all cfg output/dump_031.8908/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_031.8908/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12