first try at implementing lammps_extract_atom_size()
This commit is contained in:
Axel Kohlmeyer
@ -318,6 +318,8 @@ class lammps(object):
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self.lib.lammps_extract_atom.argtypes = [c_void_p, c_char_p]
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self.lib.lammps_extract_atom_datatype.argtypes = [c_void_p, c_char_p]
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self.lib.lammps_extract_atom_datatype.restype = c_int
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self.lib.lammps_extract_atom_size.argtypes = [c_void_p, c_char_p, c_int]
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self.lib.lammps_extract_atom_size.restype = c_int
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self.lib.lammps_extract_fix.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int, c_int]
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@ -1070,31 +1072,59 @@ class lammps(object):
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else: return None
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return self.lib.lammps_extract_atom_datatype(self.lmp, newname)
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# -------------------------------------------------------------------------
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# extract per-atom info datatype
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def extract_atom_size(self, name, dtype):
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"""Retrieve per-atom property dimensions from LAMMPS
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This is a wrapper around the :cpp:func:`lammps_extract_atom_size`
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function of the C-library interface. Its documentation includes a
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list of the supported keywords.
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This function returns ``None`` if the keyword is not
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recognized. Otherwise it will return an integer value with the size
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of the per-atom vector or array. If *name* corresponds to a per-atom
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array, the *dtype* keyword must be either LMP_SIZE_ROWS or LMP_SIZE_COLS
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from the :ref:`type <py_type_constants>` constants defined in the
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:py:mod:`lammps` module. The return value is the requested size.
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If *name* corresponds to a per-atom vector the *dtype* keyword is ignored.
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:param name: name of the property
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:type name: string
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:param type: either LMP_SIZE_ROWS or LMP_SIZE_COLS for arrays, otherwise ignored
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:type type: int
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:return: data type of per-atom property (see :ref:`py_datatype_constants`)
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:rtype: int
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"""
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if name: newname = name.encode()
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else: return None
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return self.lib.lammps_extract_atom_size(self.lmp, newname, dtype)
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# -------------------------------------------------------------------------
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# extract per-atom info
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def extract_atom(self, name, dtype=LAMMPS_AUTODETECT):
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"""Retrieve per-atom properties from LAMMPS
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This is a wrapper around the :cpp:func:`lammps_extract_atom`
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function of the C-library interface. Its documentation includes a
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list of the supported keywords and their data types.
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Since Python needs to know the data type to be able to interpret
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the result, by default, this function will try to auto-detect the data type
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by asking the library. You can also force a specific data type by setting ``dtype``
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to one of the :ref:`data type <py_datatype_constants>` constants defined in the
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:py:mod:`lammps` module.
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This function returns ``None`` if either the keyword is not
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recognized, or an invalid data type constant is used.
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This is a wrapper around the :cpp:func:`lammps_extract_atom` function of the
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C-library interface. Its documentation includes a list of the supported
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keywords and their data types. Since Python needs to know the data type to
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be able to interpret the result, by default, this function will try to
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auto-detect the data type by asking the library. You can also force a
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specific data type by setting ``dtype`` to one of the :ref:`data type
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<py_datatype_constants>` constants defined in the :py:mod:`lammps` module.
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This function returns ``None`` if either the keyword is not recognized, or
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an invalid data type constant is used.
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.. note::
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While the returned arrays of per-atom data are dimensioned
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for the range [0:nmax] - as is the underlying storage -
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the data is usually only valid for the range of [0:nlocal],
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unless the property of interest is also updated for ghost
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atoms. In some cases, this depends on a LAMMPS setting, see
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for example :doc:`comm_modify vel yes <comm_modify>`.
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While the returned vectors or arrays of per-atom data are dimensioned for
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the range [0:nmax] - as is the underlying storage - the data is usually
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only valid for the range of [0:nlocal], unless the property of interest
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is also updated for ghost atoms. In some cases, this depends on a LAMMPS
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setting, see for example :doc:`comm_modify vel yes <comm_modify>`.
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The actual size can be determined by calling
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py:meth:`extract_atom_size() <lammps.lammps.extract_atom_size>`.
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:param name: name of the property
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:type name: string
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@ -1105,6 +1135,7 @@ class lammps(object):
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ctypes.POINTER(ctypes.c_int64), ctypes.POINTER(ctypes.POINTER(ctypes.c_int64)),
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ctypes.POINTER(ctypes.c_double), ctypes.POINTER(ctypes.POINTER(ctypes.c_double)),
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or NoneType
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"""
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if dtype == LAMMPS_AUTODETECT:
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dtype = self.extract_atom_datatype(name)
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@ -2522,3 +2553,8 @@ class lammps(object):
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newcomputeid = computeid.encode()
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idx = self.lib.lammps_find_compute_neighlist(self.lmp, newcomputeid, reqid)
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return idx
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# Local Variables:
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# fill-column: 80
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# End:
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@ -54,7 +54,8 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def extract_atom(self, name, dtype=LAMMPS_AUTODETECT, nelem=LAMMPS_AUTODETECT, dim=LAMMPS_AUTODETECT):
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def extract_atom(self, name, dtype=LAMMPS_AUTODETECT, nelem=LAMMPS_AUTODETECT,
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dim=LAMMPS_AUTODETECT):
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"""Retrieve per-atom properties from LAMMPS as NumPy arrays
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This is a wrapper around the :py:meth:`lammps.extract_atom()` method.
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@ -63,16 +64,16 @@ class numpy_wrapper:
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.. note::
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The returned arrays of per-atom data are by default dimensioned
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for the range [0:nlocal] since that data is *always* valid. The
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underlying storage for the data, however, is typically allocated
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for the range of [0:nmax]. Whether there is valid data in the range
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[nlocal:nlocal+nghost] depends on whether the property of interest
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is also updated for ghost atoms. This is not often the case. In
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some cases, it depends on a LAMMPS setting, see for example
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:doc:`comm_modify vel yes <comm_modify>`. By using the optional
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*nelem* parameter the size of the returned NumPy can be overridden.
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There is no check whether the number of elements chosen is valid.
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The returned vectors or arrays of per-atom data are dimensioned
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according to the return value of :py:meth:`lammps.extract_atom_size()`.
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Except for the "mass" property, the underlying storage will always be
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dimensioned for the range [0:nmax]. The actual usable data may be
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only in the range [0:nlocal] or [0:nlocal][0:dim]. Whether there is
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valid data in the range [nlocal:nlocal+nghost] or [nlocal:local+nghost][0:dim]
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depends on whether the property of interest is also updated for ghost atoms.
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Also the value of *dim* depends on the value of *name*. By using the optional
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*nelem* and *dim* parameters the dimensions of the returned NumPy array can
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be overridden. There is no check whether the number of elements chosen is valid.
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:param name: name of the property
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:type name: string
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@ -89,21 +90,10 @@ class numpy_wrapper:
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dtype = self.lmp.extract_atom_datatype(name)
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if nelem == LAMMPS_AUTODETECT:
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if name == "mass":
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nelem = self.lmp.extract_global("ntypes") + 1
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else:
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nelem = self.lmp.extract_global("nlocal")
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nelem = self.lmp.extract_atom_size(name, LMP_SIZE_ROWS)
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if dim == LAMMPS_AUTODETECT:
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if dtype in (LAMMPS_INT_2D, LAMMPS_DOUBLE_2D, LAMMPS_INT64_2D):
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# TODO add other fields
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if name in ("x", "v", "f", "x0","omega", "angmom", "torque", "csforce", "vforce", "vest"):
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dim = 3
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elif name == "smd_data_9":
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dim = 9
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elif name == "smd_stress":
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dim = 6
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else:
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dim = 2
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dim = self.lmp.extract_atom_size(name, LMP_SIZE_COLS)
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else:
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dim = 1
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@ -119,37 +109,6 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def extract_atom_iarray(self, name, nelem, dim=1):
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warnings.warn("deprecated, use extract_atom instead", DeprecationWarning)
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if name in ['id', 'molecule']:
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c_int_type = self.lmp.c_tagint
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elif name in ['image']:
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c_int_type = self.lmp.c_imageint
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else:
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c_int_type = c_int
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if dim == 1:
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raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT)
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else:
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raw_ptr = self.lmp.extract_atom(name, LAMMPS_INT_2D)
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return self.iarray(c_int_type, raw_ptr, nelem, dim)
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# -------------------------------------------------------------------------
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def extract_atom_darray(self, name, nelem, dim=1):
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warnings.warn("deprecated, use extract_atom instead", DeprecationWarning)
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if dim == 1:
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raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE)
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else:
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raw_ptr = self.lmp.extract_atom(name, LAMMPS_DOUBLE_2D)
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return self.darray(raw_ptr, nelem, dim)
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# -------------------------------------------------------------------------
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def extract_compute(self, cid, cstyle, ctype):
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"""Retrieve data from a LAMMPS compute
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