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 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 20.635729721855316*${_u_distance} variable xmax_converted equal 20.635729721855316*1 variable ymin_converted equal -41.27550644326944*${_u_distance} variable ymin_converted equal -41.27550644326944*1 variable ymax_converted equal 41.27550644326944*${_u_distance} variable ymax_converted equal 41.27550644326944*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 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 20.6357297218553 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6357297218553 -41.2755064432694 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6357297218553 -41.2755064432694 41.2755064432694 ${zmin_converted} ${zmax_converted} units box region whole block 0 20.6357297218553 -41.2755064432694 41.2755064432694 0 ${zmax_converted} units box region whole block 0 20.6357297218553 -41.2755064432694 41.2755064432694 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -41.2755 0) to (20.6357 41.2755 4.047) 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 41.2755064432694 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 5 -1 0 orient y 1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.76209 4.76209 4.047 create_atoms 1 region upper Created 210 atoms create_atoms CPU = 0.000203133 secs group upper type 1 210 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.294558781116753 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -41.2755064432694 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 5 1 0 orient y -1 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.76209 4.76209 4.047 create_atoms 2 region lower Created 210 atoms create_atoms CPU = 6.50883e-05 secs group lower type 2 210 atoms in group lower displace_atoms lower move -2.294558781116753 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' 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*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 10 atoms, new total = 410 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1365.3108 0 -1365.3108 594.82401 214 0 -1372.0203 0 -1372.0203 -5491.738 Loop time of 2.8599 on 1 procs for 214 steps with 410 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 = -1365.31083281 -1372.02029308 -1372.02029308 Force two-norm initial, final = 12.1541 7.00606e-06 Force max component initial, final = 3.56599 9.79358e-07 Final line search alpha, max atom move = 1 9.79358e-07 Iterations, force evaluations = 214 421 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8465 | 2.8465 | 2.8465 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081182 | 0.0081182 | 0.0081182 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005258 | | | 0.18 Nlocal: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3211 ave 3211 max 3211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17448 ave 17448 max 17448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34896 ave 34896 max 34896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34896 Ave neighs/atom = 85.1122 Neighbor list builds = 0 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 214 0 -1372.0203 0 -1372.0203 -5491.738 6894.0653 1214 0 -1372.0796 0 -1372.0796 -1375.6092 6856.5526 Loop time of 13.5226 on 1 procs for 1000 steps with 410 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 = -1372.02029308 -1372.07962046 -1372.07962046 Force two-norm initial, final = 28.5265 0.000491834 Force max component initial, final = 23.447 0.00022558 Final line search alpha, max atom move = 1 0.00022558 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.365 | 13.365 | 13.365 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.035821 | 0.035821 | 0.035821 | 0.0 | 0.26 Output | 1.812e-05 | 1.812e-05 | 1.812e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1213 | | | 0.90 Nlocal: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3246 ave 3246 max 3246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17480 ave 17480 max 17480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34960 ave 34960 max 34960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34960 Ave neighs/atom = 85.2683 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 9.714 | 9.714 | 9.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1372.0796 0 -1372.0796 -1375.6092 Loop time of 9.53674e-07 on 1 procs for 0 steps with 410 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: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3246 ave 3246 max 3246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17504 ave 17504 max 17504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35008 ave 35008 max 35008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35008 Ave neighs/atom = 85.3854 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) = 9.714 | 9.714 | 9.714 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 -1372.0796 -1372.0796 20.607749 82.551013 4.0304437 -1375.6092 -1375.6092 -0.05263997 -4126.7378 -0.03717242 2.4371574 395.02403 Loop time of 9.53674e-07 on 1 procs for 0 steps with 410 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: 410 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3246 ave 3246 max 3246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17504 ave 17504 max 17504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35008 ave 35008 max 35008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35008 Ave neighs/atom = 85.3854 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_022.6199/numatoms.out 410 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1372.07962045684-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1372.07962045684-410*${isolated_atom_energy} variable adjusted_pe_metal equal -1372.07962045684-410*0 print "${adjusted_pe_metal} eV" file output/dump_022.6199/energy.out -1372.07962045684 eV print "${mindist_metal} Angstroms" file output/dump_022.6199/mindistance.out 2.43715735811808 Angstroms write_dump all cfg output/dump_022.6199/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_022.6199/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:16