python: doc and example updates
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Richard Berger
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Richard Berger
Richard Berger
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@ -2,14 +2,8 @@ System properties
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=================
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Similar to what is described in :doc:`Library_properties`, the instances of
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:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
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:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract different kinds
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of information about the active LAMMPS instance and also to modify some of it. The
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main difference between the interfaces is how the information is exposed.
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While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
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:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
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information as objects and properties.
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:py:class:`lammps <lammps.lammps>` can be used to extract different kinds
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of information about the active LAMMPS instance and also to modify some of it.
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In some cases the data returned is a direct reference to the original data
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inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
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@ -25,113 +19,38 @@ against invalid accesses.
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accordingly. These arrays can change sizes and order at every neighbor list
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rebuild and atom sort event as atoms are migrating between subdomains.
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.. tabs::
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.. code-block:: python
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.. tab:: lammps API
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from lammps import lammps
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.. code-block:: python
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lmp = lammps()
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lmp.file("in.sysinit")
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from lammps import lammps
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natoms = lmp.get_natoms()
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print(f"running simulation with {natoms} atoms")
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lmp = lammps()
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lmp.file("in.sysinit")
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lmp.command("run 1000 post no");
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natoms = lmp.get_natoms()
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print(f"running simulation with {natoms} atoms")
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for i in range(10):
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lmp.command("run 100 pre no post no")
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pe = lmp.get_thermo("pe")
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ke = lmp.get_thermo("ke")
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print(f"PE = {pe}\nKE = {ke}")
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lmp.command("run 1000 post no");
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lmp.close()
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for i in range(10):
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lmp.command("run 100 pre no post no")
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pe = lmp.get_thermo("pe")
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ke = lmp.get_thermo("ke")
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print(f"PE = {pe}\nKE = {ke}")
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**Methods**:
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lmp.close()
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* :py:meth:`version() <lammps.lammps.version()>`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
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* :py:meth:`get_thermo() <lammps.lammps.get_thermo()>`: return current value of a thermo keyword
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* :py:meth:`last_thermo() <lammps.lammps.last_thermo()>`: return a dictionary of the last thermodynamic output
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* :py:meth:`get_natoms() <lammps.lammps.get_natoms()>`: total # of atoms as int
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* :py:meth:`reset_box() <lammps.lammps.reset_box()>`: reset the simulation box size
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* :py:meth:`extract_setting() <lammps.lammps.extract_setting()>`: return a global setting
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* :py:meth:`extract_global() <lammps.lammps.extract_global()>`: extract a global quantity
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* :py:meth:`extract_box() <lammps.lammps.extract_box()>`: extract box info
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* :py:meth:`create_atoms() <lammps.lammps.create_atoms()>`: create N atoms with IDs, types, x, v, and image flags
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**Methods**:
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**Properties**:
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* :py:meth:`version() <lammps.lammps.version()>`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
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* :py:meth:`get_thermo() <lammps.lammps.get_thermo()>`: return current value of a thermo keyword
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* :py:meth:`last_thermo() <lammps.lammps.last_thermo()>`: return a dictionary of the last thermodynamic output
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* :py:meth:`get_natoms() <lammps.lammps.get_natoms()>`: total # of atoms as int
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* :py:meth:`reset_box() <lammps.lammps.reset_box()>`: reset the simulation box size
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* :py:meth:`extract_setting() <lammps.lammps.extract_setting()>`: return a global setting
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* :py:meth:`extract_global() <lammps.lammps.extract_global()>`: extract a global quantity
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* :py:meth:`extract_box() <lammps.lammps.extract_box()>`: extract box info
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* :py:meth:`create_atoms() <lammps.lammps.create_atoms()>`: create N atoms with IDs, types, x, v, and image flags
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**Properties**:
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* :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed
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.. tab:: PyLammps/IPyLammps API
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In addition to the functions provided by :py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>` objects
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have several properties which allow you to query the system state:
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L.system
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Is a dictionary describing the system such as the bounding box or number of atoms
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L.system.xlo, L.system.xhi
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bounding box limits along x-axis
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L.system.ylo, L.system.yhi
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bounding box limits along y-axis
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L.system.zlo, L.system.zhi
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bounding box limits along z-axis
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L.communication
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configuration of communication subsystem, such as the number of threads or processors
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L.communication.nthreads
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number of threads used by each LAMMPS process
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L.communication.nprocs
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number of MPI processes used by LAMMPS
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L.fixes
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List of fixes in the current system
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L.computes
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List of active computes in the current system
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L.dump
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List of active dumps in the current system
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L.groups
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List of groups present in the current system
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**Retrieving the value of an arbitrary LAMMPS expressions**
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LAMMPS expressions can be immediately evaluated by using the ``eval`` method. The
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passed string parameter can be any expression containing global :doc:`thermo` values,
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variables, compute or fix data (see :doc:`Howto_output`):
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.. code-block:: python
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result = L.eval("ke") # kinetic energy
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result = L.eval("pe") # potential energy
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result = L.eval("v_t/2.0")
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**Example**
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.. code-block:: python
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from lammps import PyLammps
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L = PyLammps()
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L.file("in.sysinit")
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print(f"running simulation with {L.system.natoms} atoms")
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L.run(1000, "post no");
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for i in range(10):
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L.run(100, "pre no post no")
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pe = L.eval("pe")
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ke = L.eval("ke")
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print(f"PE = {pe}\nKE = {ke}")
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* :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed
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