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 4.049763545393944*${_u_distance} variable lattice_constant_converted equal 4.049763545393944*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 62.86923675724095*${_u_distance} variable xmax_converted equal 62.86923675724095*1 variable ymin_converted equal -62.873286520786344*${_u_distance} variable ymin_converted equal -62.873286520786344*1 variable ymax_converted equal 62.873286520786344*${_u_distance} variable ymax_converted equal 62.873286520786344*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049763545393944*${_u_distance} variable zmax_converted equal 4.049763545393944*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04976354539394 Lattice spacing in x,y,z = 4.04976 4.04976 4.04976 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 62.8692367572409 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.8692367572409 -62.8732865207863 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.8692367572409 -62.8732865207863 62.8732865207863 ${zmin_converted} ${zmax_converted} units box region whole block 0 62.8692367572409 -62.8732865207863 62.8732865207863 0 ${zmax_converted} units box region whole block 0 62.8692367572409 -62.8732865207863 62.8732865207863 0 4.04976354539394 units box create_box 2 whole Created orthogonal box = (0 -62.8733 0) to (62.8692 62.8733 4.04976) 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 62.8732865207863 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9565 4.9565 4.04976 create_atoms 1 region upper Created 965 atoms create_atoms CPU = 0.000247002 secs group upper type 1 965 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.985878613317011 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -62.8732865207863 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 lattice fcc 4.04976354539394 orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9565 4.9565 4.04976 create_atoms 2 region lower Created 965 atoms create_atoms CPU = 0.000144005 secs group lower type 2 965 atoms in group lower displace_atoms lower move -6.985878613317011 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_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*4.04976354539394 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02488177269697 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 15 29 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1904 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 15 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6288.4062 0 -6288.4062 -490.56265 98 0 -6302.4671 0 -6302.4671 -5560.9069 Loop time of 1.75961 on 1 procs for 98 steps with 1904 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -6288.40616923 -6302.46713817 -6302.46713817 Force two-norm initial, final = 16.2238 0.0390286 Force max component initial, final = 3.42588 0.00711995 Final line search alpha, max atom move = 7.62939e-06 5.43209e-08 Iterations, force evaluations = 98 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7205 | 1.7205 | 1.7205 | 0.0 | 97.78 Neigh | 0.015484 | 0.015484 | 0.015484 | 0.0 | 0.88 Comm | 0.015033 | 0.015033 | 0.015033 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008559 | | | 0.49 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11876 ave 11876 max 11876 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: 327168 ave 327168 max 327168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327168 Ave neighs/atom = 171.832 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) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -6302.4671 0 -6302.4671 -5560.9069 32015.775 124 0 -6302.8403 0 -6302.8403 -483.45679 31798.766 Loop time of 0.652415 on 1 procs for 26 steps with 1904 atoms 101.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -6302.46713817 -6302.84029693 -6302.84029693 Force two-norm initial, final = 153.021 0.0520092 Force max component initial, final = 111.138 0.0306185 Final line search alpha, max atom move = 3.13354e-06 9.59443e-08 Iterations, force evaluations = 26 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62986 | 0.62986 | 0.62986 | 0.0 | 96.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049515 | 0.0049515 | 0.0049515 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0176 | | | 2.70 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11886 ave 11886 max 11886 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: 328266 ave 328266 max 328266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328266 Ave neighs/atom = 172.409 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 15 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 6.139 | 6.139 | 6.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6302.8403 0 -6302.8403 -483.45679 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11901 ave 11901 max 11901 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: 329226 ave 329226 max 329226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329226 Ave neighs/atom = 172.913 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) = 6.139 | 6.139 | 6.139 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 -6302.8403 -6302.8403 62.63677 125.74657 4.0372418 -483.45679 -483.45679 1.5370061 -1451.5415 -0.36586272 2.5809782 1029.3506 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1904 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: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11901 ave 11901 max 11901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164613 ave 164613 max 164613 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 329226 ave 329226 max 329226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329226 Ave neighs/atom = 172.913 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_029.8628/numatoms.out 1904 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6302.8402969307-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6302.8402969307-1904*${isolated_atom_energy} variable adjusted_pe_metal equal -6302.8402969307-1904*0 print "${adjusted_pe_metal} eV" file output/dump_029.8628/energy.out -6302.8402969307 eV print "${mindist_metal} Angstroms" file output/dump_029.8628/mindistance.out 2.58097820715796 Angstroms write_dump all cfg output/dump_029.8628/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_029.8628/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:02