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 4.049994595348835*${_u_distance} variable lattice_constant_converted equal 4.049994595348835*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 59.79745359522712*${_u_distance} variable xmax_converted equal 59.79745359522712*1 variable ymin_converted equal -59.80150358982247*${_u_distance} variable ymin_converted equal -59.80150358982247*1 variable ymax_converted equal 59.80150358982247*${_u_distance} variable ymax_converted equal 59.80150358982247*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049994595348835*${_u_distance} variable zmax_converted equal 4.049994595348835*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04999459534883 Lattice spacing in x,y,z = 4.04999 4.04999 4.04999 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 59.7974535952271 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7974535952271 -59.8015035898225 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7974535952271 -59.8015035898225 59.8015035898225 ${zmin_converted} ${zmax_converted} units box region whole block 0 59.7974535952271 -59.8015035898225 59.8015035898225 0 ${zmax_converted} units box region whole block 0 59.7974535952271 -59.8015035898225 59.8015035898225 0 4.04999459534883 units box create_box 2 whole Created orthogonal box = (0 -59.8015 0) to (59.7975 59.8015 4.04999) 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 59.8015035898225 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 -7 0 orient y 7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.486 5.486 4.04999 create_atoms 1 region upper Created 873 atoms create_atoms CPU = 0.000360966 secs group upper type 1 873 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.64417037710503 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -59.8015035898225 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 lattice fcc 4.04999459534883 orient x 13 7 0 orient y -7 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.486 5.486 4.04999 create_atoms 2 region lower Created 873 atoms create_atoms CPU = 0.000262022 secs group lower type 2 873 atoms in group lower displace_atoms lower move -6.64417037710503 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style adp pair_coeff * * ./SM_667696763561_000-files/b'AlCu.adp' Al Al Reading potential file ./SM_667696763561_000-files/b'AlCu.adp' with DATE: 2011-06-20 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*4.04999459534883 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02499729767441 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 = 15 29 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Deleted 25 atoms, new total = 1721 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 = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual 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) = 7.924 | 7.924 | 7.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5748.7921 0 -5748.7921 -2042.8386 247 0 -5766.8463 0 -5766.8463 -6095.6639 Loop time of 3.38476 on 1 procs for 247 steps with 1721 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 = -5748.79213493 -5766.84627665 -5766.84627665 Force two-norm initial, final = 14.1451 3.53494e-06 Force max component initial, final = 3.32589 7.38513e-07 Final line search alpha, max atom move = 1 7.38513e-07 Iterations, force evaluations = 247 484 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3343 | 3.3343 | 3.3343 | 0.0 | 98.51 Neigh | 0.0031099 | 0.0031099 | 0.0031099 | 0.0 | 0.09 Comm | 0.029263 | 0.029263 | 0.029263 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01807 | | | 0.53 Nlocal: 1721 ave 1721 max 1721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10759 ave 10759 max 10759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119661 ave 119661 max 119661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119661 Ave neighs/atom = 69.5299 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) = 7.924 | 7.924 | 7.924 Mbytes Step Temp E_pair E_mol TotEng Press Volume 247 0 -5766.8463 0 -5766.8463 -6095.6639 28965.38 1247 0 -5767.2275 0 -5767.2275 -705.15177 28764.605 Loop time of 14.4228 on 1 procs for 1000 steps with 1721 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 = -5766.84627665 -5767.22752195 -5767.22752196 Force two-norm initial, final = 154.796 0.0085106 Force max component initial, final = 110.926 0.00793582 Final line search alpha, max atom move = 0.167544 0.0013296 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.911 | 13.911 | 13.911 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11306 | 0.11306 | 0.11306 | 0.0 | 0.78 Output | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.399 | | | 2.77 Nlocal: 1721 ave 1721 max 1721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10764 ave 10764 max 10764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119722 ave 119722 max 119722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119722 Ave neighs/atom = 69.5654 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 -5.87828410947289e-10 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 = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton 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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 7.556 | 7.556 | 7.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5767.2275 0 -5767.2275 -705.15177 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1721 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: 1721 ave 1721 max 1721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10769 ave 10769 max 10769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119747 ave 119747 max 119747 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119747 Ave neighs/atom = 69.5799 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) = 7.556 | 7.556 | 7.556 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 -5767.2275 -5767.2275 59.604139 119.60301 4.0349662 -705.15177 -705.15177 -0.11999531 -2115.7757 0.44038153 2.5774396 1195.7149 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1721 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: 1721 ave 1721 max 1721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10769 ave 10769 max 10769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119747 ave 119747 max 119747 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 239494 ave 239494 max 239494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239494 Ave neighs/atom = 139.16 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.6015/numatoms.out 1721 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5767.227521958-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5767.227521958-1721*${isolated_atom_energy} variable adjusted_pe_metal equal -5767.227521958-1721*-5.87828410947289e-10 print "${adjusted_pe_metal} eV" file output/dump_056.6015/energy.out -5767.22752094635 eV print "${mindist_metal} Angstroms" file output/dump_056.6015/mindistance.out 2.57743961638177 Angstroms write_dump all cfg output/dump_056.6015/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_056.6015/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:17