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 83.03748843504543*${_u_distance} variable xmax_converted equal 83.03748843504543*1 variable ymin_converted equal -83.04153543460424*${_u_distance} variable ymin_converted equal -83.04153543460424*1 variable ymax_converted equal 83.04153543460424*${_u_distance} variable ymax_converted equal 83.04153543460424*1 variable zmin_converted equal 0.0*${_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 83.0374884350454 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0374884350454 -83.0415354346042 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0374884350454 -83.0415354346042 83.0415354346042 ${zmin_converted} ${zmax_converted} units box region whole block 0 83.0374884350454 -83.0415354346042 83.0415354346042 0 ${zmax_converted} units box region whole block 0 83.0374884350454 -83.0415354346042 83.0415354346042 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -83.0415 0) to (83.0375 83.0415 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 83.0415354346042 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71992 5.71992 4.047 create_atoms 1 region upper Created 1686 atoms create_atoms CPU = 0.000386 secs group upper type 1 1686 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -83.0415354346042 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.71992 5.71992 4.047 create_atoms 2 region lower Created 1686 atoms create_atoms CPU = 0.000317097 secs group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 24 47 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 38 atoms, new total = 3334 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 = 24 47 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) = 26.92 | 26.92 | 26.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11133.639 0 -11133.639 213.65219 300 0 -11177.617 0 -11177.617 -5267.9303 Loop time of 25.7888 on 1 procs for 300 steps with 3334 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 = -11133.6388758 -11177.6169898 -11177.6169898 Force two-norm initial, final = 24.442 2.0964e-05 Force max component initial, final = 4.63393 4.53792e-06 Final line search alpha, max atom move = 1 4.53792e-06 Iterations, force evaluations = 300 585 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.695 | 25.695 | 25.695 | 0.0 | 99.64 Neigh | 0.015217 | 0.015217 | 0.015217 | 0.0 | 0.06 Comm | 0.045185 | 0.045185 | 0.045185 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03346 | | | 0.13 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15707 ave 15707 max 15707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142180 ave 142180 max 142180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284360 ave 284360 max 284360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284360 Ave neighs/atom = 85.2909 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) = 26.92 | 26.92 | 26.92 Mbytes Step Temp E_pair E_mol TotEng Press Volume 300 0 -11177.617 0 -11177.617 -5267.9303 55812.661 1300 0 -11178.005 0 -11178.005 -1375.0213 55531.666 Loop time of 87.4297 on 1 procs for 1000 steps with 3334 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 = -11177.6169898 -11178.0052381 -11178.0052381 Force two-norm initial, final = 214.336 0.00897546 Force max component initial, final = 161.143 0.00883767 Final line search alpha, max atom move = 0.147655 0.00130492 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 86.779 | 86.779 | 86.779 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1444 | 0.1444 | 0.1444 | 0.0 | 0.17 Output | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5066 | | | 0.58 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15714 ave 15714 max 15714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142202 ave 142202 max 142202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284404 ave 284404 max 284404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284404 Ave neighs/atom = 85.3041 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 = 24 47 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) = 24.67 | 24.67 | 24.67 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11178.005 0 -11178.005 -1375.0213 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15736 ave 15736 max 15736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142340 ave 142340 max 142340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284680 ave 284680 max 284680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284680 Ave neighs/atom = 85.3869 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) = 24.67 | 24.67 | 24.67 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 -11178.005 -11178.005 82.782511 166.08307 4.0390269 -1375.0213 -1375.0213 0.25419787 -4125.3483 0.030265689 2.4953076 1227.2046 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15736 ave 15736 max 15736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142340 ave 142340 max 142340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284680 ave 284680 max 284680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284680 Ave neighs/atom = 85.3869 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11178.0052381226-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -11178.0052381226-3334*${isolated_atom_energy} variable adjusted_pe_metal equal -11178.0052381226-3334*0 print "${adjusted_pe_metal} eV" file output/dump_086.0501/energy.out -11178.0052381226 eV print "${mindist_metal} Angstroms" file output/dump_086.0501/mindistance.out 2.49530762642268 Angstroms write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:01:53