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 4.049696564674378*${_u_distance} variable lattice_constant_converted equal 4.049696564674378*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 52.64605534076692*${_u_distance} variable xmax_converted equal 52.64605534076692*1 variable ymin_converted equal -52.65010503733159*${_u_distance} variable ymin_converted equal -52.65010503733159*1 variable ymax_converted equal 52.65010503733159*${_u_distance} variable ymax_converted equal 52.65010503733159*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.049696564674378*${_u_distance} variable zmax_converted equal 4.049696564674378*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04969656467438 Lattice spacing in x,y,z = 4.0497 4.0497 4.0497 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 52.6460553407669 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6460553407669 -52.6501050373316 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6460553407669 -52.6501050373316 52.6501050373316 ${zmin_converted} ${zmax_converted} units box region whole block 0 52.6460553407669 -52.6501050373316 52.6501050373316 0 ${zmax_converted} units box region whole block 0 52.6460553407669 -52.6501050373316 52.6501050373316 0 4.04969656467438 units box create_box 2 whole Created orthogonal box = (0 -52.6501 0) to (52.6461 52.6501 4.0497) 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 52.6501050373316 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 12 -5 0 orient y 5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29576 5.29576 4.0497 create_atoms 1 region upper Created 677 atoms create_atoms CPU = 0.000219822 secs group upper type 1 677 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 5.85 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -52.6501050373316 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 lattice fcc 4.04969656467438 orient x 12 5 0 orient y -5 12 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.29576 5.29576 4.0497 create_atoms 2 region lower Created 677 atoms create_atoms CPU = 0.000108004 secs group lower type 2 677 atoms in group lower displace_atoms lower move -5.85 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_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*4.04969656467438 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02484828233719 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 14 28 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 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 1332 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4452.7578 0 -4452.7578 1309.9866 380 0 -4476.2745 0 -4476.2745 -5345.4285 Loop time of 2.29447 on 1 procs for 380 steps with 1332 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 = -4452.75783392 -4476.27454126 -4476.27454126 Force two-norm initial, final = 40.803 1.6788e-05 Force max component initial, final = 8.44504 3.56383e-06 Final line search alpha, max atom move = 1 3.56383e-06 Iterations, force evaluations = 380 744 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2334 | 2.2334 | 2.2334 | 0.0 | 97.34 Neigh | 0.0062518 | 0.0062518 | 0.0062518 | 0.0 | 0.27 Comm | 0.033331 | 0.033331 | 0.033331 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0215 | | | 0.94 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8434 ave 8434 max 8434 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: 157394 ave 157394 max 157394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157394 Ave neighs/atom = 118.164 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) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 380 0 -4476.2745 0 -4476.2745 -5345.4285 22450.063 1380 0 -4476.4649 0 -4476.4649 -820.9063 22330.076 Loop time of 6.75457 on 1 procs for 1000 steps with 1332 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 = -4476.27454126 -4476.4649205 -4476.46492053 Force two-norm initial, final = 98.1921 0.039434 Force max component initial, final = 69.4624 0.032447 Final line search alpha, max atom move = 1 0.032447 Iterations, force evaluations = 1000 1998 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3682 | 6.3682 | 6.3682 | 0.0 | 94.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.083156 | 0.083156 | 0.083156 | 0.0 | 1.23 Output | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3032 | | | 4.49 Nlocal: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7958 ave 7958 max 7958 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: 159124 ave 159124 max 159124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159124 Ave neighs/atom = 119.462 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 = 7.60004 ghost atom cutoff = 7.60004 binsize = 3.80002, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.60004 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) = 5.199 | 5.199 | 5.199 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4476.4649 0 -4476.4649 -820.9063 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8118 ave 8118 max 8118 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: 164996 ave 164996 max 164996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164996 Ave neighs/atom = 123.871 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) = 5.199 | 5.199 | 5.199 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 -4476.4649 -4476.4649 52.516556 105.30021 4.0379852 -820.9063 -820.9063 -2.3223368 -2458.8055 -1.5910248 2.610411 972.4122 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1332 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: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8118 ave 8118 max 8118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82498 ave 82498 max 82498 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164996 ave 164996 max 164996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164996 Ave neighs/atom = 123.871 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_045.2397/numatoms.out 1332 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4476.46492053116-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -4476.46492053116-1332*${isolated_atom_energy} variable adjusted_pe_metal equal -4476.46492053116-1332*0 print "${adjusted_pe_metal} eV" file output/dump_045.2397/energy.out -4476.46492053116 eV print "${mindist_metal} Angstroms" file output/dump_045.2397/mindistance.out 2.61041099133092 Angstroms write_dump all cfg output/dump_045.2397/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_045.2397/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:09