82 lines
2.7 KiB
ReStructuredText
82 lines
2.7 KiB
ReStructuredText
Per-atom properties
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===================
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Similar to what is described in :doc:`Library_atoms`, 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 atom quantities
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and modify some of them. The main difference between the interfaces is how the information
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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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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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determine the ``ctypes`` data type and cast pointers accordingly. If
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``numpy`` is installed arrays can also be extracted as numpy arrays, which
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will access the C arrays directly and have the correct dimensions to protect
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against invalid accesses.
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.. warning::
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When accessing per-atom data,
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please note that this data is the per-processor local data and indexed
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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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.. tab:: lammps API
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.. code-block:: python
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.sysinit")
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nlocal = lmp.extract_global("nlocal")
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x = lmp.extract_atom("x")
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for i in range(nlocal):
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print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
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lmp.close()
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**Methods**:
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* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
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**Numpy Methods**:
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* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
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.. tab:: PyLammps/IPyLammps API
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All atoms in the current simulation can be accessed by using the :py:attr:`PyLammps.atoms <lammps.PyLammps.atoms>` property.
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Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
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these objects provide access to their data (id, type, position, velocity, force, etc.):
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.. code-block:: python
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# access first atom
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L.atoms[0].id
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L.atoms[0].type
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# access second atom
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L.atoms[1].position
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L.atoms[1].velocity
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L.atoms[1].force
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Some attributes can be changed:
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.. code-block:: python
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# set position in 2D simulation
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L.atoms[0].position = (1.0, 0.0)
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# set position in 3D simulation
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L.atoms[0].position = (1.0, 0.0, 1.0)
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