2.3.6. System properties — LAMMPS documentation

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# 2.3.6. System properties

Similar to what is described in System properties, the instances of `lammps`, `PyLammps`, or `IPyLammps` can be used to extract different kinds of information about the active LAMMPS instance and also to modify some of it. The main difference between the interfaces is how the information is exposed.

While the `lammps` is just a thin layer that wraps C API calls, `PyLammps` and `IPyLammps` expose information as objects and properties.

In some cases the data returned is a direct reference to the original data inside LAMMPS cast to `ctypes` pointers. Where possible, the wrappers will determine the `ctypes` data type and cast pointers accordingly. If `numpy` is installed arrays can also be extracted as numpy arrays, which will access the C arrays directly and have the correct dimensions to protect against invalid accesses.

Warning

When accessing per-atom data, please note that this data is the per-processor local data and indexed accordingly. These arrays can change sizes and order at every neighbor list rebuild and atom sort event as atoms are migrating between subdomains.

    from lammps import lammps

    lmp = lammps()
    lmp.file("in.sysinit")

    natoms = lmp.get_natoms()
    print(f"running simulation with {natoms} atoms")

    lmp.command("run 1000 post no");

    for i in range(10):
       lmp.command("run 100 pre no post no")
       pe = lmp.get_thermo("pe")
       ke = lmp.get_thermo("ke")
       print(f"PE = {pe}\nKE = {ke}")

    lmp.close()

Methods:

- `version()`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902

- `get_thermo()`: return current value of a thermo keyword

- `last_thermo()`: return a dictionary of the last thermodynamic output

- `get_natoms()`: total # of atoms as int

- `reset_box()`: reset the simulation box size

- `extract_setting()`: return a global setting

- `extract_global()`: extract a global quantity

- `extract_box()`: extract box info

- `create_atoms()`: create N atoms with IDs, types, x, v, and image flags

Properties:

- `last_thermo_step`: the last timestep thermodynamic output was computed

In addition to the functions provided by `lammps`, `PyLammps` objects have several properties which allow you to query the system state:

L.system

  Is a dictionary describing the system such as the bounding box or number of atoms

L.system.xlo, L.system.xhi

  bounding box limits along x-axis

L.system.ylo, L.system.yhi

  bounding box limits along y-axis

L.system.zlo, L.system.zhi

  bounding box limits along z-axis

L.communication

  configuration of communication subsystem, such as the number of threads or processors

L.communication.nthreads

  number of threads used by each LAMMPS process

L.communication.nprocs

  number of MPI processes used by LAMMPS

L.fixes

  List of fixes in the current system

L.computes

  List of active computes in the current system

L.dump

  List of active dumps in the current system

L.groups

  List of groups present in the current system

Retrieving the value of an arbitrary LAMMPS expressions

LAMMPS expressions can be immediately evaluated by using the `eval` method. The passed string parameter can be any expression containing global thermo command values, variables, compute or fix data (see Output from LAMMPS (thermo, dumps, computes, fixes, variables)):

    result = L.eval("ke") # kinetic energy
    result = L.eval("pe") # potential energy

    result = L.eval("v_t/2.0")

Example

    from lammps import PyLammps

    L = PyLammps()
    L.file("in.sysinit")

    print(f"running simulation with {L.system.natoms} atoms")

    L.run(1000, "post no");

    for i in range(10):
       L.run(100, "pre no post no")
       pe = L.eval("pe")
       ke = L.eval("ke")
       print(f"PE = {pe}\nKE = {ke}")