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 4.066269248723984*${_u_distance} variable lattice_constant_converted equal 4.066269248723984*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 72.3978656880747*${_u_distance} variable xmax_converted equal 72.3978656880747*1 variable ymin_converted equal -72.40193195732343*${_u_distance} variable ymin_converted equal -72.40193195732343*1 variable ymax_converted equal 72.40193195732343*${_u_distance} variable ymax_converted equal 72.40193195732343*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.066269248723984*${_u_distance} variable zmax_converted equal 4.066269248723984*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06626924872398 Lattice spacing in x,y,z = 4.06627 4.06627 4.06627 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 72.3978656880747 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 72.3978656880747 -72.4019319573234 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 72.3978656880747 -72.4019319573234 72.4019319573234 ${zmin_converted} ${zmax_converted} units box region whole block 0 72.3978656880747 -72.4019319573234 72.4019319573234 0 ${zmax_converted} units box region whole block 0 72.3978656880747 -72.4019319573234 72.4019319573234 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -72.4019 0) to (72.3979 72.4019 4.06627) 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 72.4019319573234 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 14 -11 0 orient y 11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70961 5.70961 4.06627 create_atoms 1 region upper Created 1270 atoms create_atoms CPU = 0.000335932 secs group upper type 1 1270 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.012022216644183 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -72.4019319573234 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 14 11 0 orient y -11 14 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.70961 5.70961 4.06627 create_atoms 2 region lower Created 1270 atoms create_atoms CPU = 0.000226974 secs group lower type 2 1270 atoms in group lower displace_atoms lower move -8.012022216644183 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style bop pair_coeff * * ./SM_566399258279_000-files/b'AlCu.bop.table' Al Al Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 comm_modify cutoff 12.7 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*4.06626924872398 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03313462436199 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 24 47 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 26 atoms, new total = 2514 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 24 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 15.99 | 15.99 | 15.99 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8391.6939 0 -8391.6939 -8828.0068 224 0 -8424.9953 0 -8424.9953 -12407.055 Loop time of 66.7277 on 1 procs for 224 steps with 2514 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8391.69391839 -8424.99529937 -8424.99529937 Force two-norm initial, final = 13.3848 0.00547202 Force max component initial, final = 2.05202 0.00107228 Final line search alpha, max atom move = 0.000244141 2.61788e-07 Iterations, force evaluations = 224 449 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 66.615 | 66.615 | 66.615 | 0.0 | 99.83 Neigh | 0.039241 | 0.039241 | 0.039241 | 0.0 | 0.06 Comm | 0.052709 | 0.052709 | 0.052709 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02099 | | | 0.03 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25430 ave 25430 max 25430 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: 136076 ave 136076 max 136076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136076 Ave neighs/atom = 54.1273 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) = 16 | 16 | 16 Mbytes Step Temp E_pair E_mol TotEng Press Volume 224 0 -8424.9953 0 -8424.9953 -12407.055 42628.696 407 0 -8427.1261 0 -8427.1261 -4007.3599 42144.132 Loop time of 56.6484 on 1 procs for 183 steps with 2514 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -8424.99529937 -8427.12605777 -8427.12605777 Force two-norm initial, final = 390.521 0.0642962 Force max component initial, final = 355.563 0.057508 Final line search alpha, max atom move = 2.94916e-06 1.696e-07 Iterations, force evaluations = 183 381 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.487 | 56.487 | 56.487 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.042508 | 0.042508 | 0.042508 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.119 | | | 0.21 Nlocal: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25381 ave 25381 max 25381 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: 136244 ave 136244 max 136244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136244 Ave neighs/atom = 54.1941 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 24 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (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) = 14.63 | 14.63 | 14.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8427.1261 0 -8427.1261 -4007.3599 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2514 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: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25514 ave 25514 max 25514 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: 136448 ave 136448 max 136448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136448 Ave neighs/atom = 54.2753 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) = 14.63 | 14.63 | 14.63 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 -8427.1261 -8427.1261 71.505668 144.80386 4.070207 -4007.3599 -4007.3599 -0.49302107 -12023.775 2.1883772 2.456857 612.11316 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2514 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: 2514 ave 2514 max 2514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25514 ave 25514 max 25514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68224 ave 68224 max 68224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136448 ave 136448 max 136448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136448 Ave neighs/atom = 54.2753 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_076.3145/numatoms.out 2514 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8427.12605777143-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8427.12605777143-2514*${isolated_atom_energy} variable adjusted_pe_metal equal -8427.12605777143-2514*0 print "${adjusted_pe_metal} eV" file output/dump_076.3145/energy.out -8427.12605777143 eV print "${mindist_metal} Angstroms" file output/dump_076.3145/mindistance.out 2.45685696382402 Angstroms write_dump all cfg output/dump_076.3145/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_076.3145/success.out This indicates that LAMMPS ran successfully Total wall time: 0:02:04