LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) 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 4.039798453450203*${_u_distance} variable lattice_constant_converted equal 4.039798453450203*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 63.87482200464173*${_u_distance} variable xmax_converted equal 63.87482200464173*1 variable ymin_converted equal -63.87886180309518*${_u_distance} variable ymin_converted equal -63.87886180309518*1 variable ymax_converted equal 63.87886180309518*${_u_distance} variable ymax_converted equal 63.87886180309518*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.039798453450203*${_u_distance} variable zmax_converted equal 4.039798453450203*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.0397984534502 Lattice spacing in x,y,z = 4.0398 4.0398 4.0398 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 63.8748220046417 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8748220046417 -63.8788618030952 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8748220046417 -63.8788618030952 63.8788618030952 ${zmin_converted} ${zmax_converted} units box region whole block 0 63.8748220046417 -63.8788618030952 63.8788618030952 0 ${zmax_converted} units box region whole block 0 63.8748220046417 -63.8788618030952 63.8788618030952 0 4.0397984534502 units box create_box 2 whole Created orthogonal box = (0 -63.8789 0) to (63.8748 63.8789 4.0398) 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 63.8788618030952 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 13 -9 0 orient y 9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.62098 5.62098 4.0398 create_atoms 1 region upper Created 1001 atoms create_atoms CPU = 0.000304937 secs group upper type 1 1001 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.115124735378854 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -63.8788618030952 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 lattice fcc 4.0397984534502 orient x 13 9 0 orient y -9 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.62098 5.62098 4.0398 create_atoms 2 region lower Created 1001 atoms create_atoms CPU = 0.000187874 secs group lower type 2 1001 atoms in group lower displace_atoms lower move -7.115124735378854 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Al__MO_279544746097_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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*4.0397984534502 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0198992267251 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 11 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 21 atoms, new total = 1981 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 11 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.92 | 11.92 | 11.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5634.6887 0 -5634.6887 2150.5678 452 0 -5695.9127 0 -5695.9127 -5028.4633 Loop time of 13.1883 on 1 procs for 452 steps with 1981 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 = -5634.68873196 -5695.91269793 -5695.91269793 Force two-norm initial, final = 39.6276 4.1558e-05 Force max component initial, final = 7.47556 6.71162e-06 Final line search alpha, max atom move = 1 6.71162e-06 Iterations, force evaluations = 452 886 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.048 | 13.048 | 13.048 | 0.0 | 98.94 Neigh | 0.026968 | 0.026968 | 0.026968 | 0.0 | 0.20 Comm | 0.081193 | 0.081193 | 0.081193 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03192 | | | 0.24 Nlocal: 1981 ave 1981 max 1981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20489 ave 20489 max 20489 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: 785298 ave 785298 max 785298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 785298 Ave neighs/atom = 396.415 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) = 11.92 | 11.92 | 11.92 Mbytes Step Temp E_pair E_mol TotEng Press Volume 452 0 -5695.9127 0 -5695.9127 -5028.4633 32966.783 1452 0 -5696.0349 0 -5696.0349 -2424.1638 32851.645 Loop time of 29.926 on 1 procs for 1000 steps with 1981 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 = -5695.91269793 -5696.0348565 -5696.03485679 Force two-norm initial, final = 94.2896 0.0578112 Force max component initial, final = 76.6358 0.04891 Final line search alpha, max atom move = 0.0118955 0.00058181 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.25 | 29.25 | 29.25 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17915 | 0.17915 | 0.17915 | 0.0 | 0.60 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4969 | | | 1.66 Nlocal: 1981 ave 1981 max 1981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20468 ave 20468 max 20468 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: 775420 ave 775420 max 775420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 775420 Ave neighs/atom = 391.429 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:52) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 11 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 11.44 | 11.44 | 11.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5696.0349 0 -5696.0349 -2424.1638 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1981 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: 1981 ave 1981 max 1981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20496 ave 20496 max 20496 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: 795942 ave 795942 max 795942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795942 Ave neighs/atom = 401.788 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:52) Per MPI rank memory allocation (min/avg/max) = 11.44 | 11.44 | 11.44 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 -5696.0349 -5696.0349 63.730371 127.75772 4.0348139 -2424.1638 -2424.1638 1.232541 -7271.3415 -2.3823995 2.540958 642.61533 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1981 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: 1981 ave 1981 max 1981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20496 ave 20496 max 20496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397971 ave 397971 max 397971 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 795942 ave 795942 max 795942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 795942 Ave neighs/atom = 401.788 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_069.3903/numatoms.out 1981 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5696.03485679243-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -5696.03485679243-1981*${isolated_atom_energy} variable adjusted_pe_metal equal -5696.03485679243-1981*0 print "${adjusted_pe_metal} eV" file output/dump_069.3903/energy.out -5696.03485679243 eV print "${mindist_metal} Angstroms" file output/dump_069.3903/mindistance.out 2.54095797548121 Angstroms write_dump all cfg output/dump_069.3903/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_069.3903/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:43