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 4.066269248723984*${_u_distance}
variable lattice_constant_converted equal 4.066269248723984*1
variable xmin_converted equal 0.0*${_u_distance}
variable xmin_converted equal 0.0*1
variable xmax_converted equal 42.45309730443582*${_u_distance}
variable xmax_converted equal 42.45309730443582*1
variable ymin_converted equal -42.45716357368455*${_u_distance}
variable ymin_converted equal -42.45716357368455*1
variable ymax_converted equal 42.45716357368455*${_u_distance}
variable ymax_converted equal 42.45716357368455*1
variable zmin_converted equal 0.0*${_u_distance}
variable zmin_converted equal 0.0*1
variable zmax_converted equal 4.066269248723984*${_u_distance}
variable zmax_converted equal 4.066269248723984*1
lattice            fcc ${lattice_constant_converted}
lattice            fcc 4.06626924872398
Lattice spacing in x,y,z = 4.06627 4.06627 4.06627
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 42.4530973044358 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 42.4530973044358 -42.4571635736845 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box
region             whole block 0 42.4530973044358 -42.4571635736845 42.4571635736845 ${zmin_converted} ${zmax_converted} units box
region             whole block 0 42.4530973044358 -42.4571635736845 42.4571635736845 0 ${zmax_converted} units box
region             whole block 0 42.4530973044358 -42.4571635736845 42.4571635736845 0 4.06626924872398 units box
create_box         2 whole
Created orthogonal box = (0 -42.4572 0) to (42.4531 42.4572 4.06627)
  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 42.4571635736845 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1
lattice            fcc 4.06626924872398 orient x 10 -3 0 orient y 3 10 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.06321 5.06321 4.06627
create_atoms       1 region upper
Created 438 atoms
  create_atoms CPU = 0.000201941 secs
group              upper type 1
438 atoms in group upper
mass               1 26.981538*${_u_mass}
mass               1 26.981538*1
displace_atoms     upper move 4.698137929009748 0 0.3333333333333333 units lattice
region             lower block INF INF ${ymin_converted}  0.0 INF INF units box
region             lower block INF INF -42.4571635736845  0.0 INF INF units box
lattice            fcc ${lattice_constant_converted} orient x 10 3 0 orient y -3 10 0 orient z 0 0 1
lattice            fcc 4.06626924872398 orient x 10 3 0 orient y -3 10 0 orient z 0 0 1
Lattice spacing in x,y,z = 5.06321 5.06321 4.06627
create_atoms       2 region lower
Created 438 atoms
  create_atoms CPU = 7.79629e-05 secs
group              lower type 2
438 atoms in group lower
displace_atoms     lower move -4.698137929009748 0 -0.3333333333333333 units lattice
mass               2 26.981538*${_u_mass}
mass               2 26.981538*1
pair_style bop
pair_coeff * * ./SM_566399258279_000-files/b'AlCu.bop.table' Al Al
Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06
Reading potential file ./SM_566399258279_000-files/b'AlCu.bop.table' with DATE: 2015-07-06
comm_modify cutoff 12.7
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*4.06626924872398
delete_atoms       overlap ${delete_distance} all all
delete_atoms       overlap 2.03313462436199 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 = 6.2
  ghost atom cutoff = 12.7
  binsize = 3.1, bins = 14 28 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional, copy from (2)
      attributes: full, newton on
      pair build: copy
      stencil: none
      bin: none
  (2) pair bop, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
Deleted 20 atoms, new total = 856
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 = 6.2
  ghost atom cutoff = 12.7
  binsize = 3.1, bins = 14 28 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair bop, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.429 | 8.429 | 8.429 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -2845.0663            0   -2845.0663   -11573.403 
     120            0   -2859.8343            0   -2859.8343   -17772.207 
Loop time of 12.8645 on 1 procs for 120 steps with 856 atoms

100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -2845.06628224     -2859.83428434     -2859.83428434
  Force two-norm initial, final = 8.09186 0.00915207
  Force max component initial, final = 1.61598 0.00267115
  Final line search alpha, max atom move = 0.00195312 5.21708e-06
  Iterations, force evaluations = 120 246

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.812     | 12.812     | 12.812     |   0.0 | 99.59
Neigh   | 0.035302   | 0.035302   | 0.035302   |   0.0 |  0.27
Comm    | 0.013036   | 0.013036   | 0.013036   |   0.0 |  0.10
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.004447   |            |       |  0.03

Nlocal:    856 ave 856 max 856 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11604 ave 11604 max 11604 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:  46116 ave 46116 max 46116 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46116
Ave neighs/atom = 53.8738
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) = 8.428 | 8.428 | 8.428 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
     120            0   -2859.8343            0   -2859.8343   -17772.207    14658.397 
     363            0   -2861.2694            0   -2861.2694    -4211.469    14400.718 
Loop time of 26.0947 on 1 procs for 243 steps with 856 atoms

100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -2859.83428434     -2861.26939885     -2861.26939885
  Force two-norm initial, final = 203.351 0.112363
  Force max component initial, final = 167.521 0.0827518
  Final line search alpha, max atom move = 7.9706e-07 6.59582e-08
  Iterations, force evaluations = 243 498

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 26.002     | 26.002     | 26.002     |   0.0 | 99.65
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.025211   | 0.025211   | 0.025211   |   0.0 |  0.10
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.06722    |            |       |  0.26

Nlocal:    856 ave 856 max 856 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11590 ave 11590 max 11590 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:  46120 ave 46120 max 46120 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46120
Ave neighs/atom = 53.8785
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 = 6.2
  ghost atom cutoff = 12.7
  binsize = 3.1, bins = 14 28 2
  3 neighbor lists, perpetual/occasional/extra = 1 2 0
  (1) pair bop, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) compute centro/atom, occasional, copy from (1)
      attributes: full, newton on
      pair build: copy
      stencil: none
      bin: none
  (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) = 7.936 | 7.936 | 7.936 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0   -2861.2694            0   -2861.2694    -4211.469 
Loop time of 9.53674e-07 on 1 procs for 0 steps with 856 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:    856 ave 856 max 856 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11639 ave 11639 max 11639 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:  46252 ave 46252 max 46252 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46252
Ave neighs/atom = 54.0327
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) = 7.936 | 7.936 | 7.936 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   -2861.2694   -2861.2694    41.801871    84.914327     4.057023    -4211.469    -4211.469    3.9554807   -12629.177   -9.1857565     2.208085    733.20712 
Loop time of 1.19209e-06 on 1 procs for 0 steps with 856 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:    856 ave 856 max 856 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11639 ave 11639 max 11639 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    23126 ave 23126 max 23126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  46252 ave 46252 max 46252 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 46252
Ave neighs/atom = 54.0327
Neighbor list builds = 0
Dangerous builds = 0
variable           num_atoms equal "count(all)"
print              "${num_atoms}" file output/dump_033.3985/numatoms.out
856
variable  adjusted_pe_metal  equal ${pe_metal}-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -2861.26939884928-${num_atoms}*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -2861.26939884928-856*${isolated_atom_energy}
variable  adjusted_pe_metal  equal -2861.26939884928-856*0
print              "${adjusted_pe_metal} eV" file output/dump_033.3985/energy.out
-2861.26939884928 eV
print              "${mindist_metal} Angstroms" file output/dump_033.3985/mindistance.out
2.20808498213833 Angstroms
write_dump         all cfg output/dump_033.3985/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_033.3985/success.out
This indicates that LAMMPS ran successfully
Total wall time: 0:00:39