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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 68.84484159946443*${_u_distance} variable xmax_converted equal 68.84484159946443*1 variable ymin_converted equal -68.84889129602911*${_u_distance} variable ymin_converted equal -68.84889129602911*1 variable ymax_converted equal 68.84889129602911*${_u_distance} variable ymax_converted equal 68.84889129602911*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 68.8448415994644 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8448415994644 -68.8488912960291 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8448415994644 -68.8488912960291 68.8488912960291 ${zmin_converted} ${zmax_converted} units box region whole block 0 68.8448415994644 -68.8488912960291 68.8488912960291 0 ${zmax_converted} units box region whole block 0 68.8448415994644 -68.8488912960291 68.8488912960291 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -68.8489 0) to (68.8448 68.8489 4.0497) 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 68.8488912960291 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 15 -8 0 orient y 8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.479 5.479 4.0497 create_atoms 1 region upper Created 1158 atoms create_atoms CPU = 0.000463963 secs group upper type 1 1158 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.65 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -68.8488912960291 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 15 8 0 orient y -8 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.479 5.479 4.0497 create_atoms 2 region lower Created 1158 atoms create_atoms CPU = 0.000283003 secs group lower type 2 1158 atoms in group lower displace_atoms lower move -7.65 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 19 37 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 2282 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 19 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.053 | 6.053 | 6.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7643.8741 0 -7643.8741 -316.11402 402 0 -7671.4525 0 -7671.4525 -5831.2033 Loop time of 4.45917 on 1 procs for 402 steps with 2282 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 = -7643.87414936 -7671.45245737 -7671.45245737 Force two-norm initial, final = 39.7627 2.08637e-05 Force max component initial, final = 7.64961 6.48923e-06 Final line search alpha, max atom move = 1 6.48923e-06 Iterations, force evaluations = 402 796 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3486 | 4.3486 | 4.3486 | 0.0 | 97.52 Neigh | 0.015197 | 0.015197 | 0.015197 | 0.0 | 0.34 Comm | 0.058006 | 0.058006 | 0.058006 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03737 | | | 0.84 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13148 ave 13148 max 13148 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: 265372 ave 265372 max 265372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265372 Ave neighs/atom = 116.289 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) = 6.054 | 6.054 | 6.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 402 0 -7671.4525 0 -7671.4525 -5831.2033 38390.241 1402 0 -7671.8015 0 -7671.8015 -1270.75 38178.636 Loop time of 11.4088 on 1 procs for 1000 steps with 2282 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 = -7671.45245737 -7671.80153971 -7671.80153986 Force two-norm initial, final = 169.976 0.057671 Force max component initial, final = 131.864 0.0539513 Final line search alpha, max atom move = 0.0125135 0.00067512 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.78 | 10.78 | 10.78 | 0.0 | 94.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13516 | 0.13516 | 0.13516 | 0.0 | 1.18 Output | 2.2173e-05 | 2.2173e-05 | 2.2173e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4941 | | | 4.33 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13178 ave 13178 max 13178 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: 270964 ave 270964 max 270964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270964 Ave neighs/atom = 118.74 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 19 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.811 | 5.811 | 5.811 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7671.8015 0 -7671.8015 -1270.75 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2282 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: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13178 ave 13178 max 13178 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: 280280 ave 280280 max 280280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280280 Ave neighs/atom = 122.822 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) = 5.811 | 5.811 | 5.811 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 -7671.8015 -7671.8015 68.752839 137.69778 4.0327641 -1270.75 -1270.75 -0.59733517 -3813.9072 2.2546143 2.6042434 1292.1159 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2282 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 | | 2.146e-06 | | |100.00 Nlocal: 2282 ave 2282 max 2282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13178 ave 13178 max 13178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140140 ave 140140 max 140140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280280 ave 280280 max 280280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280280 Ave neighs/atom = 122.822 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_056.1450/numatoms.out 2282 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7671.8015398557-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -7671.8015398557-2282*${isolated_atom_energy} variable adjusted_pe_metal equal -7671.8015398557-2282*0 print "${adjusted_pe_metal} eV" file output/dump_056.1450/energy.out -7671.8015398557 eV print "${mindist_metal} Angstroms" file output/dump_056.1450/mindistance.out 2.60424343007954 Angstroms write_dump all cfg output/dump_056.1450/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_056.1450/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:15