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 4.073718130588532*${_u_distance} variable lattice_constant_converted equal 4.073718130588532*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 16.796370141410236*${_u_distance} variable xmax_converted equal 16.796370141410236*1 variable ymin_converted equal -50.3931841423613*${_u_distance} variable ymin_converted equal -50.3931841423613*1 variable ymax_converted equal 50.3931841423613*${_u_distance} variable ymax_converted equal 50.3931841423613*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.073718130588532*${_u_distance} variable zmax_converted equal 4.073718130588532*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.07371813058853 Lattice spacing in x,y,z = 4.07372 4.07372 4.07372 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 16.7963701414102 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.7963701414102 -50.3931841423613 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 16.7963701414102 -50.3931841423613 50.3931841423613 ${zmin_converted} ${zmax_converted} units box region whole block 0 16.7963701414102 -50.3931841423613 50.3931841423613 0 ${zmax_converted} units box region whole block 0 16.7963701414102 -50.3931841423613 50.3931841423613 0 4.07371813058853 units box create_box 2 whole Created orthogonal box = (0 -50.3932 0) to (16.7964 50.3932 4.07372) 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 50.3931841423613 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 4 -1 0 orient y 1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.94011 4.94011 4.07372 create_atoms 1 region upper Created 206 atoms create_atoms CPU = 0.000153065 secs group upper type 1 206 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 1.8553975315279474 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -50.3931841423613 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 lattice fcc 4.07371813058853 orient x 4 1 0 orient y -1 4 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.94011 4.94011 4.07372 create_atoms 2 region lower Created 206 atoms create_atoms CPU = 4.60148e-05 secs group lower type 2 206 atoms in group lower displace_atoms lower move -1.8553975315279474 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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*4.07371813058853 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03685906529426 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 4 22 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 4 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1227.0156 0 -1227.0156 4446.9549 252 0 -1235.4712 0 -1235.4712 -1432.1313 Loop time of 1.338 on 1 procs for 252 steps with 404 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1227.01557967 -1235.47119698 -1235.47119698 Force two-norm initial, final = 19.06 8.03115e-06 Force max component initial, final = 6.13499 1.25163e-06 Final line search alpha, max atom move = 1 1.25163e-06 Iterations, force evaluations = 252 499 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3131 | 1.3131 | 1.3131 | 0.0 | 98.14 Neigh | 0.0020301 | 0.0020301 | 0.0020301 | 0.0 | 0.15 Comm | 0.016128 | 0.016128 | 0.016128 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006785 | | | 0.51 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5179 ave 5179 max 5179 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: 80140 ave 80140 max 80140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80140 Ave neighs/atom = 198.366 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) = 4.51 | 4.51 | 4.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -1235.4712 0 -1235.4712 -1432.1313 6896.174 1252 0 -1235.4756 0 -1235.4756 -505.26057 6882.8608 Loop time of 4.79242 on 1 procs for 1000 steps with 404 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1235.47119698 -1235.47560115 -1235.47560115 Force two-norm initial, final = 6.41656 0.000791969 Force max component initial, final = 4.69251 0.000461445 Final line search alpha, max atom move = 1 0.000461445 Iterations, force evaluations = 1000 2000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.569 | 4.569 | 4.569 | 0.0 | 95.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.056436 | 0.056436 | 0.056436 | 0.0 | 1.18 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.167 | | | 3.48 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5560 ave 5560 max 5560 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: 80152 ave 80152 max 80152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80152 Ave neighs/atom = 198.396 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 0.143095413925774 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 4 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1235.4756 0 -1235.4756 -505.26057 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5560 ave 5560 max 5560 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: 80152 ave 80152 max 80152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80152 Ave neighs/atom = 198.396 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) = 4.648 | 4.648 | 4.648 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 -1235.4756 -1235.4756 16.782297 100.78637 4.0692633 -505.26057 -505.26057 -0.082992437 -1515.5914 -0.10729671 2.6236588 242.90848 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5560 ave 5560 max 5560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40076 ave 40076 max 40076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80152 ave 80152 max 80152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80152 Ave neighs/atom = 198.396 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_028.0725/numatoms.out 404 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1235.47560114822-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -1235.47560114822-404*${isolated_atom_energy} variable adjusted_pe_metal equal -1235.47560114822-404*0.143095413925774 print "${adjusted_pe_metal} eV" file output/dump_028.0725/energy.out -1293.28614837423 eV print "${mindist_metal} Angstroms" file output/dump_028.0725/mindistance.out 2.62365884007403 Angstroms write_dump all cfg output/dump_028.0725/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_028.0725/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06