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 3.9946166351437573*${_u_distance} variable lattice_constant_converted equal 3.9946166351437573*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 81.96268070289065*${_u_distance} variable xmax_converted equal 81.96268070289065*1 variable ymin_converted equal -81.96667531952579*${_u_distance} variable ymin_converted equal -81.96667531952579*1 variable ymax_converted equal 81.96667531952579*${_u_distance} variable ymax_converted equal 81.96667531952579*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.9946166351437573*${_u_distance} variable zmax_converted equal 3.9946166351437573*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.99461663514376 Lattice spacing in x,y,z = 3.99462 3.99462 3.99462 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 81.9626807028907 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 81.9626807028907 -81.9666753195258 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 81.9626807028907 -81.9666753195258 81.9666753195258 ${zmin_converted} ${zmax_converted} units box region whole block 0 81.9626807028907 -81.9666753195258 81.9666753195258 0 ${zmax_converted} units box region whole block 0 81.9626807028907 -81.9666753195258 81.9666753195258 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -81.9667 0) to (81.9627 81.9667 3.99462) 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 81.9666753195258 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 15 -14 0 orient y 14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64589 5.64589 3.99462 create_atoms 1 region upper Created 1686 atoms create_atoms CPU = 0.000392914 secs group upper type 1 1686 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 9.233228037907434 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -81.9666753195258 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 15 14 0 orient y -14 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.64589 5.64589 3.99462 create_atoms 2 region lower Created 1686 atoms create_atoms CPU = 0.000270844 secs group lower type 2 1686 atoms in group lower displace_atoms lower move -9.233228037907434 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001 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*3.99461663514376 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.99730831757188 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 22 44 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3334 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 22 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.56 | 10.56 | 10.56 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10906.976 0 -10906.976 325.97937 280 0 -10943.262 0 -10943.262 -3572.2958 Loop time of 11.9163 on 1 procs for 280 steps with 3334 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -10906.9760075 -10943.2624933 -10943.2624933 Force two-norm initial, final = 16.7566 0.00550783 Force max component initial, final = 3.11015 0.000502936 Final line search alpha, max atom move = 0.000244141 1.22787e-07 Iterations, force evaluations = 280 545 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.742 | 11.742 | 11.742 | 0.0 | 98.54 Neigh | 0.079141 | 0.079141 | 0.079141 | 0.0 | 0.66 Comm | 0.058117 | 0.058117 | 0.058117 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03683 | | | 0.31 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18311 ave 18311 max 18311 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: 441284 ave 441284 max 441284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441284 Ave neighs/atom = 132.359 Neighbor list builds = 7 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) = 10.56 | 10.56 | 10.56 Mbytes Step Temp E_pair E_mol TotEng Press Volume 280 0 -10943.262 0 -10943.262 -3572.2958 53673.334 297 0 -10943.538 0 -10943.538 -1654.8309 53409.765 Loop time of 1.21698 on 1 procs for 17 steps with 3334 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -10943.2624933 -10943.537664 -10943.537664 Force two-norm initial, final = 99.6014 0.082347 Force max component initial, final = 93.6709 0.0648736 Final line search alpha, max atom move = 9.43141e-07 6.11849e-08 Iterations, force evaluations = 17 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1943 | 1.1943 | 1.1943 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0051141 | 0.0051141 | 0.0051141 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01761 | | | 1.45 Nlocal: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18316 ave 18316 max 18316 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: 441480 ave 441480 max 441480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441480 Ave neighs/atom = 132.418 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 -6.30324000329931e-20 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 22 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 10.07 | 10.07 | 10.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10943.538 0 -10943.538 -1654.8309 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18311 ave 18311 max 18311 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: 441904 ave 441904 max 441904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441904 Ave neighs/atom = 132.545 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) = 10.07 | 10.07 | 10.07 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 -10943.538 -10943.538 82.068971 163.93335 3.9698524 -1654.8309 -1654.8309 1.9485904 -4967.2659 0.82465672 2.5494001 317.62836 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3334 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: 3334 ave 3334 max 3334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18311 ave 18311 max 18311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 220952 ave 220952 max 220952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 441904 ave 441904 max 441904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441904 Ave neighs/atom = 132.545 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_086.0501/numatoms.out 3334 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10943.5376639668-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -10943.5376639668-3334*${isolated_atom_energy} variable adjusted_pe_metal equal -10943.5376639668-3334*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_086.0501/energy.out -10943.5376639668 eV print "${mindist_metal} Angstroms" file output/dump_086.0501/mindistance.out 2.54940012686377 Angstroms write_dump all cfg output/dump_086.0501/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_086.0501/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:13