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 4.066269248723984*${_u_distance} variable lattice_constant_converted equal 4.066269248723984*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 63.12547417922113*${_u_distance} variable xmax_converted equal 63.12547417922113*1 variable ymin_converted equal -63.129540448469854*${_u_distance} variable ymin_converted equal -63.129540448469854*1 variable ymax_converted equal 63.129540448469854*${_u_distance} variable ymax_converted equal 63.129540448469854*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.066269248723984*${_u_distance} variable zmax_converted equal 4.066269248723984*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.06626924872398 Lattice spacing in x,y,z = 4.06627 4.06627 4.06627 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 63.1254741792211 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.1254741792211 -63.1295404484699 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 63.1254741792211 -63.1295404484699 63.1295404484699 ${zmin_converted} ${zmax_converted} units box region whole block 0 63.1254741792211 -63.1295404484699 63.1295404484699 0 ${zmax_converted} units box region whole block 0 63.1254741792211 -63.1295404484699 63.1295404484699 0 4.06626924872398 units box create_box 2 whole Created orthogonal box = (0 -63.1295 0) to (63.1255 63.1295 4.06627) 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 63.1295404484699 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9767 4.9767 4.06627 create_atoms 1 region upper Created 965 atoms create_atoms CPU = 0.000252008 secs group upper type 1 965 atoms in group upper mass 1 26.981538*${_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 -63.1295404484699 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 lattice fcc 4.06626924872398 orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.9767 4.9767 4.06627 create_atoms 2 region lower Created 965 atoms create_atoms CPU = 0.000160933 secs group lower type 2 965 atoms in group lower displace_atoms lower move -6.985878613317011 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style bop pair_coeff * * ./SM_566399258279_000-files/b'AlCu.bop.table' Al Al Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06 comm_modify cutoff 12.7 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*4.06626924872398 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.03313462436199 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 21 41 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 21 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 14.57 | 14.57 | 14.57 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6350.1947 0 -6350.1947 -9851.6617 200 0 -6373.9289 0 -6373.9289 -14287.469 Loop time of 57.6133 on 1 procs for 200 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 = -6350.19472193 -6373.9288561 -6373.9288561 Force two-norm initial, final = 8.93108 0.00531809 Force max component initial, final = 1.21908 0.00188453 Final line search alpha, max atom move = 0.000976562 1.84036e-06 Iterations, force evaluations = 200 506 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 57.483 | 57.483 | 57.483 | 0.0 | 99.77 Neigh | 0.064473 | 0.064473 | 0.064473 | 0.0 | 0.11 Comm | 0.04786 | 0.04786 | 0.04786 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01751 | | | 0.03 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20517 ave 20517 max 20517 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: 102690 ave 102690 max 102690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102690 Ave neighs/atom = 53.9338 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) = 14.59 | 14.59 | 14.59 Mbytes Step Temp E_pair E_mol TotEng Press Volume 200 0 -6373.9289 0 -6373.9289 -14287.469 32408.834 982 0 -6376.263 0 -6376.263 -3436.296 31947.986 Loop time of 181.941 on 1 procs for 782 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 = -6373.9288561 -6376.26297801 -6376.26297801 Force two-norm initial, final = 367.273 0.235884 Force max component initial, final = 323.244 0.200651 Final line search alpha, max atom move = 1.18269e-07 2.37307e-08 Iterations, force evaluations = 782 1581 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 181.37 | 181.37 | 181.37 | 0.0 | 99.69 Neigh | 0.033164 | 0.033164 | 0.033164 | 0.0 | 0.02 Comm | 0.14296 | 0.14296 | 0.14296 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3962 | | | 0.22 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20643 ave 20643 max 20643 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: 102904 ave 102904 max 102904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102904 Ave neighs/atom = 54.0462 Neighbor list builds = 1 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 = 6.2 ghost atom cutoff = 12.7 binsize = 3.1, bins = 21 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair bop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (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) = 13.22 | 13.22 | 13.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6376.263 0 -6376.263 -3436.296 Loop time of 1.19209e-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 | | 1.192e-06 | | |100.00 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20643 ave 20643 max 20643 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: 102880 ave 102880 max 102880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102880 Ave neighs/atom = 54.0336 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) = 13.22 | 13.22 | 13.22 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 -6376.263 -6376.263 62.225255 126.25908 4.0664382 -3436.296 -3436.296 0.42888603 -10319.38 10.062963 2.3287511 1074.377 Loop time of 1.19209e-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 | | 1.192e-06 | | |100.00 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20643 ave 20643 max 20643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51440 ave 51440 max 51440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102880 ave 102880 max 102880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102880 Ave neighs/atom = 54.0336 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -6376.26297801457-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6376.26297801457-1904*${isolated_atom_energy} variable adjusted_pe_metal equal -6376.26297801457-1904*0 print "${adjusted_pe_metal} eV" file output/dump_029.8628/energy.out -6376.26297801457 eV print "${mindist_metal} Angstroms" file output/dump_029.8628/mindistance.out 2.32875111314411 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: 0:04:00