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 4.210700303316116*${_u_distance} variable lattice_constant_converted equal 4.210700303316116*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 69.69949203653441*${_u_distance} variable xmax_converted equal 69.69949203653441*1 variable ymin_converted equal -69.70370273683773*${_u_distance} variable ymin_converted equal -69.70370273683773*1 variable ymax_converted equal 69.70370273683773*${_u_distance} variable ymax_converted equal 69.70370273683773*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.210700303316116*${_u_distance} variable zmax_converted equal 4.210700303316116*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.21070030331612 Lattice spacing in x,y,z = 4.2107 4.2107 4.2107 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 69.6994920365344 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 69.6994920365344 -69.7037027368377 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 69.6994920365344 -69.7037027368377 69.7037027368377 ${zmin_converted} ${zmax_converted} units box region whole block 0 69.6994920365344 -69.7037027368377 69.7037027368377 0 ${zmax_converted} units box region whole block 0 69.6994920365344 -69.7037027368377 69.7037027368377 0 4.21070030331612 units box create_box 2 whole Created orthogonal box = (0 -69.7037 0) to (69.6995 69.7037 4.2107) 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 69.7037027368377 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 15 -7 0 orient y 7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59631 5.59631 4.2107 create_atoms 1 region upper Created 1098 atoms create_atoms CPU = 0.00039196 secs group upper type 1 1098 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 7.448825410761081 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -69.7037027368377 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 lattice fcc 4.21070030331612 orient x 15 7 0 orient y -7 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.59631 5.59631 4.2107 create_atoms 2 region lower Created 1098 atoms create_atoms CPU = 0.000294924 secs group lower type 2 1098 atoms in group lower displace_atoms lower move -7.448825410761081 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_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*4.21070030331612 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.10535015165806 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 ghost atom cutoff = 9 binsize = 4.5, bins = 16 31 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2168 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 ghost atom cutoff = 9 binsize = 4.5, bins = 16 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8056.8943 0 -8056.8943 91.873248 332 0 -8071.4681 0 -8071.4681 -2105.8593 Loop time of 9.16289 on 1 procs for 332 steps with 2168 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 = -8056.89430774 -8071.46806586 -8071.46806586 Force two-norm initial, final = 20.7231 1.94568e-05 Force max component initial, final = 4.69708 2.1099e-06 Final line search alpha, max atom move = 1 2.1099e-06 Iterations, force evaluations = 332 657 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.069 | 9.069 | 9.069 | 0.0 | 98.98 Neigh | 0.012093 | 0.012093 | 0.012093 | 0.0 | 0.13 Comm | 0.051353 | 0.051353 | 0.051353 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0304 | | | 0.33 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13341 ave 13341 max 13341 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: 373248 ave 373248 max 373248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 373248 Ave neighs/atom = 172.162 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) = 6.063 | 6.063 | 6.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 332 0 -8071.4681 0 -8071.4681 -2105.8593 40913.797 1332 0 -8071.5891 0 -8071.5891 -279.90009 40720.18 Loop time of 26.2158 on 1 procs for 1000 steps with 2168 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 = -8071.46806586 -8071.58908847 -8071.5890885 Force two-norm initial, final = 71.8127 0.0110703 Force max component initial, final = 51.9675 0.00800827 Final line search alpha, max atom move = 0.0320742 0.000256859 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.597 | 25.597 | 25.597 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14132 | 0.14132 | 0.14132 | 0.0 | 0.54 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4779 | | | 1.82 Nlocal: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13690 ave 13690 max 13690 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: 374272 ave 374272 max 374272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374272 Ave neighs/atom = 172.635 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 16 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.203 | 6.203 | 6.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8071.5891 0 -8071.5891 -279.90009 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13919 ave 13919 max 13919 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: 375024 ave 375024 max 375024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375024 Ave neighs/atom = 172.982 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) = 6.203 | 6.203 | 6.203 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 -8071.5891 -8071.5891 69.512698 139.40741 4.2020353 -279.90009 -279.90009 -0.31424889 -839.59688 0.21086773 2.6770516 1391.2003 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2168 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: 2168 ave 2168 max 2168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13919 ave 13919 max 13919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187512 ave 187512 max 187512 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 375024 ave 375024 max 375024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375024 Ave neighs/atom = 172.982 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_050.0338/numatoms.out 2168 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8071.589088504-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -8071.589088504-2168*${isolated_atom_energy} variable adjusted_pe_metal equal -8071.589088504-2168*0 print "${adjusted_pe_metal} eV" file output/dump_050.0338/energy.out -8071.589088504 eV print "${mindist_metal} Angstroms" file output/dump_050.0338/mindistance.out 2.67705156160016 Angstroms write_dump all cfg output/dump_050.0338/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_050.0338/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:35