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 4.05000014603138*${_u_distance} variable lattice_constant_converted equal 4.05000014603138*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 75.3343574291807*${_u_distance} variable xmax_converted equal 75.3343574291807*1 variable ymin_converted equal -75.33840742932674*${_u_distance} variable ymin_converted equal -75.33840742932674*1 variable ymax_converted equal 75.33840742932674*${_u_distance} variable ymax_converted equal 75.33840742932674*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.05000014603138*${_u_distance} variable zmax_converted equal 4.05000014603138*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000014603138 Lattice spacing in x,y,z = 4.05 4.05 4.05 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 75.3343574291807 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 75.3343574291807 -75.3384074293267 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 75.3343574291807 -75.3384074293267 75.3384074293267 ${zmin_converted} ${zmax_converted} units box region whole block 0 75.3343574291807 -75.3384074293267 75.3384074293267 0 ${zmax_converted} units box region whole block 0 75.3343574291807 -75.3384074293267 75.3384074293267 0 4.05000014603138 units box create_box 2 whole Created orthogonal box = (0 -75.3384 0) to (75.3344 75.3384 4.05) 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 75.3384074293267 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 15 -11 0 orient y 11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.66096 5.66096 4.05 create_atoms 1 region upper Created 1386 atoms create_atoms CPU = 0.000347853 secs group upper type 1 1386 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 8.370483856982224 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -75.3384074293267 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 lattice fcc 4.05000014603138 orient x 15 11 0 orient y -11 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.66096 5.66096 4.05 create_atoms 2 region lower Created 1386 atoms create_atoms CPU = 0.000238895 secs group lower type 2 1386 atoms in group lower displace_atoms lower move -8.370483856982224 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_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*4.05000014603138 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500007301569 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 18 36 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 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2738 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 18 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.08 | 10.08 | 10.08 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9155.6089 0 -9155.6089 -1584.0942 323 0 -9179.6766 0 -9179.6766 -5930.4682 Loop time of 6.57332 on 1 procs for 323 steps with 2738 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9155.60892046 -9179.67656048 -9179.67656048 Force two-norm initial, final = 14.9807 3.23819e-05 Force max component initial, final = 2.42973 7.62239e-06 Final line search alpha, max atom move = 1 7.62239e-06 Iterations, force evaluations = 323 638 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4609 | 6.4609 | 6.4609 | 0.0 | 98.29 Neigh | 0.018369 | 0.018369 | 0.018369 | 0.0 | 0.28 Comm | 0.057284 | 0.057284 | 0.057284 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03672 | | | 0.56 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15907 ave 15907 max 15907 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: 384948 ave 384948 max 384948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384948 Ave neighs/atom = 140.595 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) = 10.08 | 10.08 | 10.08 Mbytes Step Temp E_pair E_mol TotEng Press Volume 323 0 -9179.6766 0 -9179.6766 -5930.4682 45972.123 1323 0 -9180.1194 0 -9180.1194 -1323.0134 45701.276 Loop time of 20.9965 on 1 procs for 1000 steps with 2738 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -9179.67656048 -9180.1193829 -9180.11938302 Force two-norm initial, final = 211.126 0.0551969 Force max component initial, final = 153.416 0.0360703 Final line search alpha, max atom move = 0.0310439 0.00111976 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.232 | 20.232 | 20.232 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16501 | 0.16501 | 0.16501 | 0.0 | 0.79 Output | 2.2888e-05 | 2.2888e-05 | 2.2888e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5994 | | | 2.85 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15912 ave 15912 max 15912 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: 384968 ave 384968 max 384968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384968 Ave neighs/atom = 140.602 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 = 8.49954 ghost atom cutoff = 8.49954 binsize = 4.24977, bins = 18 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.49954 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) = 9.595 | 9.595 | 9.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9180.1194 0 -9180.1194 -1323.0134 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2738 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: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15927 ave 15927 max 15927 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: 385528 ave 385528 max 385528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 385528 Ave neighs/atom = 140.806 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) = 9.595 | 9.595 | 9.595 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 -9180.1194 -9180.1194 75.140479 150.67681 4.0365277 -1323.0134 -1323.0134 1.2612842 -3971.3324 1.0308153 2.4880119 1096.9785 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2738 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 | | 1.907e-06 | | |100.00 Nlocal: 2738 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15927 ave 15927 max 15927 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 192764 ave 192764 max 192764 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 385528 ave 385528 max 385528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 385528 Ave neighs/atom = 140.806 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_072.5077/numatoms.out 2738 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9180.11938301909-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -9180.11938301909-2738*${isolated_atom_energy} variable adjusted_pe_metal equal -9180.11938301909-2738*0 print "${adjusted_pe_metal} eV" file output/dump_072.5077/energy.out -9180.11938301909 eV print "${mindist_metal} Angstroms" file output/dump_072.5077/mindistance.out 2.48801190033644 Angstroms write_dump all cfg output/dump_072.5077/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_072.5077/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:27