Merge branch 'develop' into python-lint
This commit is contained in:
Axel Kohlmeyer
@ -58,7 +58,8 @@ 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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@ -67,16 +68,16 @@ 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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@ -93,21 +94,10 @@ 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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@ -123,37 +113,6 @@ 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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@ -275,11 +234,11 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def gather_bonds(self):
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"""Retrieve global list of bonds as NumPy array
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"""Retrieve global list of bonds as a NumPy array
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.. versionadded:: 28Jul2021
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This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
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This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`.
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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@ -293,11 +252,11 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def gather_angles(self):
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""" Retrieve global list of angles as NumPy array
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""" Retrieve global list of angles as a NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
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This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`.
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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@ -311,11 +270,11 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def gather_dihedrals(self):
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""" Retrieve global list of dihedrals as NumPy array
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""" Retrieve global list of dihedrals as a NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
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This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`.
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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@ -329,11 +288,11 @@ class numpy_wrapper:
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# -------------------------------------------------------------------------
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def gather_impropers(self):
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""" Retrieve global list of impropers as NumPy array
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""" Retrieve global list of impropers as a NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
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This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`.
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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