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 4.045259781181812*${_u_distance} variable lattice_constant_converted equal 4.045259781181812*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 62.79931953482105*${_u_distance} variable xmax_converted equal 62.79931953482105*1 variable ymin_converted equal -62.80336479460223*${_u_distance} variable ymin_converted equal -62.80336479460223*1 variable ymax_converted equal 62.80336479460223*${_u_distance} variable ymax_converted equal 62.80336479460223*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.045259781181812*${_u_distance} variable zmax_converted equal 4.045259781181812*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04525978118181 Lattice spacing in x,y,z = 4.04526 4.04526 4.04526 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 62.7993195348211 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.7993195348211 -62.8033647946022 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 62.7993195348211 -62.8033647946022 62.8033647946022 ${zmin_converted} ${zmax_converted} units box region whole block 0 62.7993195348211 -62.8033647946022 62.8033647946022 0 ${zmax_converted} units box region whole block 0 62.7993195348211 -62.8033647946022 62.8033647946022 0 4.04525978118181 units box create_box 2 whole Created orthogonal box = (0 -62.8034 0) to (62.7993 62.8034 4.04526) 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 62.8033647946022 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 15 -4 0 orient y 4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95098 4.95098 4.04526 create_atoms 1 region upper Created 965 atoms create_atoms CPU = 0.000354052 secs group upper type 1 965 atoms in group upper mass 1 26.981538*${_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 -62.8033647946022 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 lattice fcc 4.04525978118181 orient x 15 4 0 orient y -4 15 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.95098 4.95098 4.04526 create_atoms 2 region lower Created 965 atoms create_atoms CPU = 0.000228882 secs group lower type 2 965 atoms in group lower displace_atoms lower move -6.985878613317011 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_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*4.04525978118181 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.0226298905909 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 30 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 8.5 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.616 | 5.616 | 5.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6462.8877 0 -6462.8877 -1871.7448 237 0 -6475.7161 0 -6475.7161 -5351.3115 Loop time of 3.30744 on 1 procs for 237 steps with 1904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6462.88768723 -6475.71612491 -6475.71612491 Force two-norm initial, final = 13.6222 1.02229e-05 Force max component initial, final = 2.81693 3.11025e-06 Final line search alpha, max atom move = 1 3.11025e-06 Iterations, force evaluations = 237 455 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2462 | 3.2462 | 3.2462 | 0.0 | 98.15 Neigh | 0.012744 | 0.012744 | 0.012744 | 0.0 | 0.39 Comm | 0.030011 | 0.030011 | 0.030011 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01849 | | | 0.56 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11796 ave 11796 max 11796 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: 266822 ave 266822 max 266822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266822 Ave neighs/atom = 140.138 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) = 5.616 | 5.616 | 5.616 Mbytes Step Temp E_pair E_mol TotEng Press Volume 237 0 -6475.7161 0 -6475.7161 -5351.3115 31909.079 1237 0 -6476.0339 0 -6476.0339 -666.36681 31719.604 Loop time of 14.4624 on 1 procs for 1000 steps with 1904 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -6475.71612491 -6476.03393133 -6476.03393134 Force two-norm initial, final = 147.813 0.0165545 Force max component initial, final = 110.95 0.00860328 Final line search alpha, max atom move = 0.123345 0.00106117 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.912 | 13.912 | 13.912 | 0.0 | 96.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1203 | 0.1203 | 0.1203 | 0.0 | 0.83 Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4305 | | | 2.98 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11801 ave 11801 max 11801 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: 266816 ave 266816 max 266816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266816 Ave neighs/atom = 140.134 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.755 | 5.755 | 5.755 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6476.0339 0 -6476.0339 -666.36681 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: 11816 ave 11816 max 11816 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: 267136 ave 267136 max 267136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267136 Ave neighs/atom = 140.303 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) = 5.755 | 5.755 | 5.755 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 -6476.0339 -6476.0339 62.653976 125.60673 4.0305677 -666.36681 -666.36681 0.34245057 -1999.8759 0.43297856 2.4641921 1103.9649 Loop time of 1.90735e-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 | | 1.907e-06 | | |100.00 Nlocal: 1904 ave 1904 max 1904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11816 ave 11816 max 11816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133568 ave 133568 max 133568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267136 ave 267136 max 267136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267136 Ave neighs/atom = 140.303 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}*${isolated_atom_energy} variable adjusted_pe_metal equal -6476.03393134036-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6476.03393134036-1904*${isolated_atom_energy} variable adjusted_pe_metal equal -6476.03393134036-1904*0 print "${adjusted_pe_metal} eV" file output/dump_029.8628/energy.out -6476.03393134036 eV print "${mindist_metal} Angstroms" file output/dump_029.8628/mindistance.out 2.46419214525058 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: 0:00:17