LAMMPS (8 Feb 2023)
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode

variable        files index 2uo2 3uo2 4uo2

mdi             connect

label LOOP

  units           metal
  atom_style      full

  read_data       data.${files}
  read_data       data.2uo2
Reading data file ...
  triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  6 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.002 seconds

  neighbor        0.3 bin
  neigh_modify    every 1 delay 0 check yes

  timestep        0.001

  fix             1 all mdi/qm virial yes elements U O connect no

  thermo_style    custom step temp pe etotal press
  thermo          1

  run             0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2348)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.239 | 5.239 | 5.239 Mbytes
   Step          Temp          PotEng         TotEng         Press     
         0   0             -50.539026     -50.539026     -120855.18    
Loop time of 4.37e-07 on 1 procs for 0 steps with 6 atoms

228.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Bond    | 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   |            | 4.37e-07   |            |       |100.00

Nlocal:              6 ave           6 max           6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              2 ave           2 max           2 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

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

  #write_dump      all custom dump.series.mpi.${files}   #                id type x y z fx fy fz modify sort id

  clear

next            files

jump            SELF LOOP

  units           metal
  atom_style      full

  read_data       data.${files}
  read_data       data.3uo2
Reading data file ...
  triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  9 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.001 seconds

  neighbor        0.3 bin
  neigh_modify    every 1 delay 0 check yes

  timestep        0.001

  fix             1 all mdi/qm virial yes elements U O connect no

  thermo_style    custom step temp pe etotal press
  thermo          1

  run             0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2348)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.239 | 5.239 | 5.239 Mbytes
   Step          Temp          PotEng         TotEng         Press     
         0   0             -78.155585     -78.155585     -99929.253    
Loop time of 4.69e-07 on 1 procs for 0 steps with 9 atoms

213.2% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Bond    | 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   |            | 4.69e-07   |            |       |100.00

Nlocal:              9 ave           9 max           9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              3 ave           3 max           3 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

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

  #write_dump      all custom dump.series.mpi.${files}   #                id type x y z fx fy fz modify sort id

  clear

next            files

jump            SELF LOOP

  units           metal
  atom_style      full

  read_data       data.${files}
  read_data       data.4uo2
Reading data file ...
  triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  12 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.001 seconds

  neighbor        0.3 bin
  neigh_modify    every 1 delay 0 check yes

  timestep        0.001

  fix             1 all mdi/qm virial yes elements U O connect no

  thermo_style    custom step temp pe etotal press
  thermo          1

  run             0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2348)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.239 | 5.239 | 5.239 Mbytes
   Step          Temp          PotEng         TotEng         Press     
         0   0             -102.35715     -102.35715     -31036.694    
Loop time of 4.2e-07 on 1 procs for 0 steps with 12 atoms

0.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Bond    | 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   |            | 4.2e-07    |            |       |100.00

Nlocal:             12 ave          12 max          12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              5 ave           5 max           5 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

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0

  #write_dump      all custom dump.series.mpi.${files}   #                id type x y z fx fy fz modify sort id

  clear

next            files

jump            SELF LOOP

mdi             exit
Total wall time: 0:00:00
