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 3.869337007403374*${_u_distance} variable lattice_constant_converted equal 3.869337007403374*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 58.16889002010141*${_u_distance} variable xmax_converted equal 58.16889002010141*1 variable ymin_converted equal -58.17275935710881*${_u_distance} variable ymin_converted equal -58.17275935710881*1 variable ymax_converted equal 58.17275935710881*${_u_distance} variable ymax_converted equal 58.17275935710881*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.869337007403374*${_u_distance} variable zmax_converted equal 3.869337007403374*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.86933700740337 Lattice spacing in x,y,z = 3.86934 3.86934 3.86934 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 58.1688900201014 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 58.1688900201014 -58.1727593571088 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 58.1688900201014 -58.1727593571088 58.1727593571088 ${zmin_converted} ${zmax_converted} units box region whole block 0 58.1688900201014 -58.1727593571088 58.1727593571088 0 ${zmax_converted} units box region whole block 0 58.1688900201014 -58.1727593571088 58.1727593571088 0 3.86933700740337 units box create_box 2 whole Created orthogonal box = (0 -58.1728 0) to (58.1689 58.1728 3.86934) 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 58.1727593571088 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 lattice fcc 3.86933700740337 orient x 15 -1 0 orient y 1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.11815 4.11815 3.86934 create_atoms 1 region upper Created 906 atoms create_atoms CPU = 0.000307083 secs group upper type 1 906 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.764983370267808 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -58.1727593571088 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 lattice fcc 3.86933700740337 orient x 15 1 0 orient y -1 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.11815 4.11815 3.86934 create_atoms 2 region lower Created 906 atoms create_atoms CPU = 0.000181198 secs group lower type 2 906 atoms in group lower displace_atoms lower move -6.764983370267808 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000 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*3.86933700740337 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.93466850370169 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, 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 kim, perpetual attributes: full, newton off, cut 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1784 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.593 | 5.593 | 5.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5676.1549 0 -5676.1549 -3943.7104 364 0 -5703.8066 0 -5703.8066 -13992.881 Loop time of 4.66148 on 1 procs for 364 steps with 1784 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 = -5676.15485788 -5703.80661323 -5703.80661323 Force two-norm initial, final = 26.6734 2.12375e-07 Force max component initial, final = 7.44864 2.52058e-08 Final line search alpha, max atom move = 1 2.52058e-08 Iterations, force evaluations = 364 716 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5765 | 4.5765 | 4.5765 | 0.0 | 98.18 Neigh | 0.012024 | 0.012024 | 0.012024 | 0.0 | 0.26 Comm | 0.0467 | 0.0467 | 0.0467 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02621 | | | 0.56 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11434 ave 11434 max 11434 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: 260220 ave 260220 max 260220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260220 Ave neighs/atom = 145.863 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) = 5.595 | 5.595 | 5.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 364 0 -5703.8066 0 -5703.8066 -13992.881 26186.472 1364 0 -5704.5219 0 -5704.5219 -3336.6469 25990.097 Loop time of 13.7368 on 1 procs for 1000 steps with 1784 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -5703.80661323 -5704.52187481 -5704.52187484 Force two-norm initial, final = 267.035 0.0398188 Force max component initial, final = 189.785 0.0367001 Final line search alpha, max atom move = 0.0584892 0.00214656 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.192 | 13.192 | 13.192 | 0.0 | 96.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12142 | 0.12142 | 0.12142 | 0.0 | 0.88 Output | 1.4067e-05 | 1.4067e-05 | 1.4067e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.423 | | | 3.08 Nlocal: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11475 ave 11475 max 11475 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: 259472 ave 259472 max 259472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259472 Ave neighs/atom = 145.444 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 = 8.19533 ghost atom cutoff = 8.19533 binsize = 4.09766, bins = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19533 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) = 5.733 | 5.733 | 5.733 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5704.5219 0 -5704.5219 -3336.6469 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11536 ave 11536 max 11536 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: 280952 ave 280952 max 280952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280952 Ave neighs/atom = 157.484 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) = 5.733 | 5.733 | 5.733 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 -5704.5219 -5704.5219 57.943889 116.34552 3.8552327 -3336.6469 -3336.6469 0.17986321 -10012.375 2.2541567 2.5301519 213.67246 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1784 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: 1784 ave 1784 max 1784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11536 ave 11536 max 11536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140476 ave 140476 max 140476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280952 ave 280952 max 280952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280952 Ave neighs/atom = 157.484 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_007.6281/numatoms.out 1784 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5704.52187484479-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5704.52187484479-1784*${isolated_atom_energy} variable adjusted_pe_metal equal -5704.52187484479-1784*0 print "${adjusted_pe_metal} eV" file output/dump_007.6281/energy.out -5704.52187484479 eV print "${mindist_metal} Angstroms" file output/dump_007.6281/mindistance.out 2.53015190870973 Angstroms write_dump all cfg output/dump_007.6281/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_007.6281/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:18