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 4.050000071525574*${_u_distance} variable lattice_constant_converted equal 4.050000071525574*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 65.92922457855579*${_u_distance} variable xmax_converted equal 65.92922457855579*1 variable ymin_converted equal -65.93327457862732*${_u_distance} variable ymin_converted equal -65.93327457862732*1 variable ymax_converted equal 65.93327457862732*${_u_distance} variable ymax_converted equal 65.93327457862732*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050000071525574*${_u_distance} variable zmax_converted equal 4.050000071525574*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05000007152557 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 65.9292245785558 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292245785558 -65.9332745786273 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292245785558 -65.9332745786273 65.9332745786273 ${zmin_converted} ${zmax_converted} units box region whole block 0 65.9292245785558 -65.9332745786273 65.9332745786273 0 ${zmax_converted} units box region whole block 0 65.9292245785558 -65.9332745786273 65.9332745786273 0 4.05000007152557 units box create_box 2 whole Created orthogonal box = (0 -65.9333 0) to (65.9292 65.9333 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 65.9332745786273 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 12 -11 0 orient y 11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72216 5.72216 4.05 create_atoms 1 region upper Created 1062 atoms create_atoms CPU = 0.0004282 secs group upper type 1 1062 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.325469268244868 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -65.9332745786273 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 lattice fcc 4.05000007152557 orient x 12 11 0 orient y -11 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.72216 5.72216 4.05 create_atoms 2 region lower Created 1062 atoms create_atoms CPU = 0.00028801 secs group lower type 2 1062 atoms in group lower displace_atoms lower move -7.325469268244868 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005 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*4.05000007152557 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500003576279 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 18 35 2 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2092 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 18 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7002.2851 0 -7002.2851 -2176.6814 347 0 -7022.0311 0 -7022.0311 -6350.484 Loop time of 3.43915 on 1 procs for 347 steps with 2092 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 = -7002.28511619 -7022.031085 -7022.031085 Force two-norm initial, final = 16.5222 3.17624e-06 Force max component initial, final = 3.19934 6.72869e-07 Final line search alpha, max atom move = 1 6.72869e-07 Iterations, force evaluations = 347 679 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3521 | 3.3521 | 3.3521 | 0.0 | 97.47 Neigh | 0.012833 | 0.012833 | 0.012833 | 0.0 | 0.37 Comm | 0.044826 | 0.044826 | 0.044826 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0294 | | | 0.85 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12231 ave 12231 max 12231 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: 267628 ave 267628 max 267628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267628 Ave neighs/atom = 127.929 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press Volume 347 0 -7022.0311 0 -7022.0311 -6350.484 35210.131 1347 0 -7022.3717 0 -7022.3717 -1771.956 35000.629 Loop time of 10.7072 on 1 procs for 1000 steps with 2092 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 = -7022.031085 -7022.37172196 -7022.37172201 Force two-norm initial, final = 160.577 0.0263381 Force max component initial, final = 117.596 0.0199107 Final line search alpha, max atom move = 0.147386 0.00293455 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.118 | 10.118 | 10.118 | 0.0 | 94.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12648 | 0.12648 | 0.12648 | 0.0 | 1.18 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4625 | | | 4.32 Nlocal: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12237 ave 12237 max 12237 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: 267140 ave 267140 max 267140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267140 Ave neighs/atom = 127.696 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 18 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.77 | 5.77 | 5.77 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7022.3717 0 -7022.3717 -1771.956 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12255 ave 12255 max 12255 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: 269068 ave 269068 max 269068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269068 Ave neighs/atom = 128.618 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) = 5.77 | 5.77 | 5.77 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 -7022.3717 -7022.3717 65.719444 131.86655 4.0387534 -1771.956 -1771.956 -0.90852461 -5314.5414 -0.41809642 2.5848703 496.83651 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2092 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: 2092 ave 2092 max 2092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12255 ave 12255 max 12255 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134534 ave 134534 max 134534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269068 ave 269068 max 269068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269068 Ave neighs/atom = 128.618 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_085.0209/numatoms.out 2092 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.37172200776-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.37172200776-2092*${isolated_atom_energy} variable adjusted_pe_metal equal -7022.37172200776-2092*0 print "${adjusted_pe_metal} eV" file output/dump_085.0209/energy.out -7022.37172200776 eV print "${mindist_metal} Angstroms" file output/dump_085.0209/mindistance.out 2.58487031255226 Angstroms write_dump all cfg output/dump_085.0209/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_085.0209/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:14