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 36.17279211043727*${_u_distance} variable xmax_converted equal 36.17279211043727*1 variable ymin_converted equal -72.34957883750968*${_u_distance} variable ymin_converted equal -72.34957883750968*1 variable ymax_converted equal 72.34957883750968*${_u_distance} variable ymax_converted equal 72.34957883750968*1 variable zmin_converted equal 0.0*${_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 36.1727921104373 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 36.1727921104373 -72.3495788375097 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 36.1727921104373 -72.3495788375097 72.3495788375097 ${zmin_converted} ${zmax_converted} units box region whole block 0 36.1727921104373 -72.3495788375097 72.3495788375097 0 ${zmax_converted} units box region whole block 0 36.1727921104373 -72.3495788375097 72.3495788375097 0 3.99461663514376 units box create_box 2 whole Created orthogonal box = (0 -72.3496 0) to (36.1728 72.3496 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 72.3495788375097 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 -1 0 orient y 1 9 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 9 -1 0 orient y 1 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.41132 4.41132 3.99462 create_atoms 1 region upper Created 658 atoms create_atoms CPU = 0.000314951 secs group upper type 1 658 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.074923312161837 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -72.3495788375097 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 9 1 0 orient y -1 9 0 orient z 0 0 1 lattice fcc 3.99461663514376 orient x 9 1 0 orient y -1 9 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.41132 4.41132 3.99462 create_atoms 2 region lower Created 658 atoms create_atoms CPU = 0.000139952 secs group lower type 2 658 atoms in group lower displace_atoms lower move -4.074923312161837 0 -0.3333333333333333 units lattice mass 2 26.981538*${_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 = 10 38 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 16 atoms, new total = 1300 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 = 10 38 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4253.4634 0 -4253.4634 255.07099 266 0 -4262.3103 0 -4262.3103 -2732.556 Loop time of 4.59065 on 1 procs for 266 steps with 1300 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 = -4253.46342397 -4262.31028168 -4262.31028168 Force two-norm initial, final = 10.6061 7.02594e-06 Force max component initial, final = 2.92278 8.50292e-07 Final line search alpha, max atom move = 1 8.50292e-07 Iterations, force evaluations = 266 526 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.544 | 4.544 | 4.544 | 0.0 | 98.98 Neigh | 0.0041811 | 0.0041811 | 0.0041811 | 0.0 | 0.09 Comm | 0.027045 | 0.027045 | 0.027045 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01547 | | | 0.34 Nlocal: 1300 ave 1300 max 1300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8872 ave 8872 max 8872 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: 170884 ave 170884 max 170884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170884 Ave neighs/atom = 131.449 Neighbor list builds = 1 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 266 0 -4262.3103 0 -4262.3103 -2732.556 20908.513 355 0 -4262.3796 0 -4262.3796 -804.46312 20805.488 Loop time of 1.70759 on 1 procs for 89 steps with 1300 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4262.31028168 -4262.37956843 -4262.37956843 Force two-norm initial, final = 39.1877 0.0149836 Force max component initial, final = 28.4596 0.00739863 Final line search alpha, max atom move = 3.33506e-05 2.46749e-07 Iterations, force evaluations = 89 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6679 | 1.6679 | 1.6679 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0091724 | 0.0091724 | 0.0091724 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03055 | | | 1.79 Nlocal: 1300 ave 1300 max 1300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8851 ave 8851 max 8851 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: 170936 ave 170936 max 170936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170936 Ave neighs/atom = 131.489 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 = 10 38 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4262.3796 0 -4262.3796 -804.46312 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1300 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: 1300 ave 1300 max 1300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8857 ave 8857 max 8857 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: 171140 ave 171140 max 171140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171140 Ave neighs/atom = 131.646 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) = 5.216 | 5.216 | 5.216 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 -4262.3796 -4262.3796 36.099069 144.69916 3.9830514 -804.46312 -804.46312 0.31387333 -2413.1351 -0.56810001 2.5219002 206.85443 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1300 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: 1300 ave 1300 max 1300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8857 ave 8857 max 8857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85570 ave 85570 max 85570 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171140 ave 171140 max 171140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171140 Ave neighs/atom = 131.646 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_012.6804/numatoms.out 1300 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4262.37956843333-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4262.37956843333-1300*${isolated_atom_energy} variable adjusted_pe_metal equal -4262.37956843333-1300*-6.30324000329931e-20 print "${adjusted_pe_metal} eV" file output/dump_012.6804/energy.out -4262.37956843333 eV print "${mindist_metal} Angstroms" file output/dump_012.6804/mindistance.out 2.52190023415675 Angstroms write_dump all cfg output/dump_012.6804/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_012.6804/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:06