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 4.050010219216347*${_u_distance} variable lattice_constant_converted equal 4.050010219216347*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 61.82072295558621*${_u_distance} variable xmax_converted equal 61.82072295558621*1 variable ymin_converted equal -61.82477296580543*${_u_distance} variable ymin_converted equal -61.82477296580543*1 variable ymax_converted equal 61.82477296580543*${_u_distance} variable ymax_converted equal 61.82477296580543*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.050010219216347*${_u_distance} variable zmax_converted equal 4.050010219216347*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.05001021921635 Lattice spacing in x,y,z = 4.05001 4.05001 4.05001 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 61.8207229555862 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.8207229555862 -61.8247729658054 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 61.8207229555862 -61.8247729658054 61.8247729658054 ${zmin_converted} ${zmax_converted} units box region whole block 0 61.8207229555862 -61.8247729658054 61.8247729658054 0 ${zmax_converted} units box region whole block 0 61.8207229555862 -61.8247729658054 61.8247729658054 0 4.05001021921635 units box create_box 2 whole Created orthogonal box = (0 -61.8248 0) to (61.8207 61.8248 4.05001) 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 61.8247729658054 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 13 -8 0 orient y 8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57182 5.57182 4.05001 create_atoms 1 region upper Created 933 atoms create_atoms CPU = 0.000261068 secs group upper type 1 933 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 6.868951885113186 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -61.8247729658054 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 lattice fcc 4.05001021921635 orient x 13 8 0 orient y -8 13 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.57182 5.57182 4.05001 create_atoms 2 region lower Created 933 atoms create_atoms CPU = 0.000155926 secs group lower type 2 933 atoms in group lower displace_atoms lower move -6.868951885113186 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_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*4.05001021921635 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02500510960818 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 17 33 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1840 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 17 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.575 | 5.575 | 5.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6192.6388 0 -6192.6388 1387.1634 336 0 -6216.6645 0 -6216.6645 -5435.6154 Loop time of 3.11571 on 1 procs for 336 steps with 1840 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6192.63876991 -6216.66454592 -6216.66454592 Force two-norm initial, final = 31.5 2.91553e-05 Force max component initial, final = 6.92986 7.25072e-06 Final line search alpha, max atom move = 1 7.25072e-06 Iterations, force evaluations = 336 654 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.027 | 3.027 | 3.027 | 0.0 | 97.15 Neigh | 0.021592 | 0.021592 | 0.021592 | 0.0 | 0.69 Comm | 0.040293 | 0.040293 | 0.040293 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02679 | | | 0.86 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10659 ave 10659 max 10659 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: 196248 ave 196248 max 196248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196248 Ave neighs/atom = 106.657 Neighbor list builds = 4 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) = 5.575 | 5.575 | 5.575 Mbytes Step Temp E_pair E_mol TotEng Press Volume 336 0 -6216.6645 0 -6216.6645 -5435.6154 30958.701 1336 0 -6216.9022 0 -6216.9022 -1374.5478 30791.491 Loop time of 9.20085 on 1 procs for 1000 steps with 1840 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -6216.66454592 -6216.90218869 -6216.90218869 Force two-norm initial, final = 120.511 0.00106418 Force max component initial, final = 89.6074 0.000926547 Final line search alpha, max atom move = 1 0.000926547 Iterations, force evaluations = 1000 1996 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6875 | 8.6875 | 8.6875 | 0.0 | 94.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11072 | 0.11072 | 0.11072 | 0.0 | 1.20 Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4026 | | | 4.38 Nlocal: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10860 ave 10860 max 10860 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: 195760 ave 195760 max 195760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195760 Ave neighs/atom = 106.391 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.79221, bins = 17 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.713 | 5.713 | 5.713 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6216.9022 0 -6216.9022 -1374.5478 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10879 ave 10879 max 10879 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: 206302 ave 206302 max 206302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206302 Ave neighs/atom = 112.121 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) = 5.713 | 5.713 | 5.713 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 -6216.9022 -6216.9022 61.746876 123.64955 4.0329533 -1374.5478 -1374.5478 -0.048153535 -4123.5922 -0.0031405859 2.5851858 980.84109 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1840 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: 1840 ave 1840 max 1840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10879 ave 10879 max 10879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103151 ave 103151 max 103151 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206302 ave 206302 max 206302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206302 Ave neighs/atom = 112.121 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_063.2150/numatoms.out 1840 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6216.90218868671-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -6216.90218868671-1840*${isolated_atom_energy} variable adjusted_pe_metal equal -6216.90218868671-1840*0 print "${adjusted_pe_metal} eV" file output/dump_063.2150/energy.out -6216.90218868671 eV print "${mindist_metal} Angstroms" file output/dump_063.2150/mindistance.out 2.58518577479309 Angstroms write_dump all cfg output/dump_063.2150/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_063.2150/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:12