LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.032988503575325*${_u_distance} variable lattice_constant_converted equal 4.032988503575325*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 29.360599488233362*${_u_distance} variable xmax_converted equal 29.360599488233362*1 variable ymin_converted equal -58.7252319649703*${_u_distance} variable ymin_converted equal -58.7252319649703*1 variable ymax_converted equal 58.7252319649703*${_u_distance} variable ymax_converted equal 58.7252319649703*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.032988503575325*${_u_distance} variable zmax_converted equal 4.032988503575325*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.03298850357533 Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 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 29.3605994882334 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.3605994882334 -58.7252319649703 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 29.3605994882334 -58.7252319649703 58.7252319649703 ${zmin_converted} ${zmax_converted} units box region whole block 0 29.3605994882334 -58.7252319649703 58.7252319649703 0 ${zmax_converted} units box region whole block 0 29.3605994882334 -58.7252319649703 58.7252319649703 0 4.03298850357533 units box create_box 2 whole Created orthogonal box = (0 -58.7252 0) to (29.3606 58.7252 4.03299) 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 58.7252319649703 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 -2 0 orient y 2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.98576 4.98576 4.03299 create_atoms 1 region upper Created 426 atoms create_atoms CPU = 0.000193834 secs group upper type 1 426 atoms in group upper mass 1 26.981538*${_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 -58.7252319649703 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 lattice fcc 4.03298850357533 orient x 7 2 0 orient y -2 7 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.98576 4.98576 4.03299 create_atoms 2 region lower Created 426 atoms create_atoms CPU = 8.10623e-05 secs group lower type 2 426 atoms in group lower displace_atoms lower move -3.276049450176233 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Al__MO_140175748626_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.03298850357533 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.01649425178767 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 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 13.7567 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.663 | 6.663 | 6.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2394.6283 0 -2394.6283 765.60011 255 0 -2420.8217 0 -2420.8217 -8849.2523 Loop time of 5.89645 on 1 procs for 255 steps with 834 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2394.62832591 -2420.82168916 -2420.82168916 Force two-norm initial, final = 18.9568 8.90518e-06 Force max component initial, final = 5.48857 1.2198e-06 Final line search alpha, max atom move = 1 1.2198e-06 Iterations, force evaluations = 255 497 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8437 | 5.8437 | 5.8437 | 0.0 | 99.11 Neigh | 0.0078878 | 0.0078878 | 0.0078878 | 0.0 | 0.13 Comm | 0.035212 | 0.035212 | 0.035212 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00963 | | | 0.16 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15014 ave 15014 max 15014 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: 551096 ave 551096 max 551096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551096 Ave neighs/atom = 660.787 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) = 6.664 | 6.664 | 6.664 Mbytes Step Temp E_pair E_mol TotEng Press Volume 255 0 -2420.8217 0 -2420.8217 -8849.2523 13907.422 1255 0 -2421.1193 0 -2421.1193 -2318.3808 13782.492 Loop time of 23.5005 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 = -2420.82168916 -2421.1193162 -2421.1193162 Force two-norm initial, final = 88.5397 0.00727148 Force max component initial, final = 67.7832 0.0071155 Final line search alpha, max atom move = 0.225584 0.00160514 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.018 | 23.018 | 23.018 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13558 | 0.13558 | 0.13558 | 0.0 | 0.58 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3473 | | | 1.48 Nlocal: 834 ave 834 max 834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15094 ave 15094 max 15094 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: 546628 ave 546628 max 546628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 546628 Ave neighs/atom = 655.429 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 6.802 | 6.802 | 6.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2421.1193 0 -2421.1193 -2318.3808 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: 15166 ave 15166 max 15166 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: 547836 ave 547836 max 547836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 547836 Ave neighs/atom = 656.878 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:52) Per MPI rank memory allocation (min/avg/max) = 6.802 | 6.802 | 6.802 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 -2421.1193 -2421.1193 29.14562 117.45046 4.0262404 -2318.3808 -2318.3808 0.82110056 -6956.1213 0.15780667 2.5626307 490.1255 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: 15166 ave 15166 max 15166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 273918 ave 273918 max 273918 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 547836 ave 547836 max 547836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 547836 Ave neighs/atom = 656.878 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -2421.11931619918-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2421.11931619918-834*${isolated_atom_energy} variable adjusted_pe_metal equal -2421.11931619918-834*0 print "${adjusted_pe_metal} eV" file output/dump_031.8908/energy.out -2421.11931619918 eV print "${mindist_metal} Angstroms" file output/dump_031.8908/mindistance.out 2.56263073124915 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: 0:00:29