From d256614c9f642e2028e8996903e3b36d56ad6164 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 15 Feb 2021 13:19:25 -0500 Subject: [PATCH] Fix docs after PR #2592 --- doc/src/Python_atoms.rst | 2 +- doc/src/Python_module.rst | 12 ++++++------ doc/src/Python_neighbor.rst | 4 ++-- doc/src/Python_objects.rst | 12 ++++++------ python/lammps/core.py | 2 +- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/doc/src/Python_atoms.rst b/doc/src/Python_atoms.rst index 92b9677d16..be0d4ff800 100644 --- a/doc/src/Python_atoms.rst +++ b/doc/src/Python_atoms.rst @@ -50,7 +50,7 @@ against invalid accesses. **Numpy Methods**: - * :py:meth:`numpy.extract_atom() `: extract a per-atom quantity as numpy array + * :py:meth:`numpy.extract_atom() `: extract a per-atom quantity as numpy array .. tab:: PyLammps/IPyLammps API diff --git a/doc/src/Python_module.rst b/doc/src/Python_module.rst index 59be645cbd..d2564986de 100644 --- a/doc/src/Python_module.rst +++ b/doc/src/Python_module.rst @@ -61,7 +61,7 @@ functions. Below is a detailed documentation of the API. .. autoclass:: lammps.lammps :members: -.. autoclass:: lammps.numpy::numpy_wrapper +.. autoclass:: lammps.numpy_wrapper::numpy_wrapper :members: ---------- @@ -134,8 +134,8 @@ Style Constants to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST` for the equivalent constants in the C library interface. Used in :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants - :py:func:`lammps.numpy.extract_compute() ` and - :py:func:`lammps.numpy.extract_fix() `. + :py:func:`lammps.numpy.extract_compute() ` and + :py:func:`lammps.numpy.extract_fix() `. .. _py_type_constants: @@ -149,8 +149,8 @@ Type Constants to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST` for the equivalent constants in the C library interface. Used in :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants - :py:func:`lammps.numpy.extract_compute() ` and - :py:func:`lammps.numpy.extract_fix() `. + :py:func:`lammps.numpy.extract_compute() ` and + :py:func:`lammps.numpy.extract_fix() `. .. _py_vartype_constants: @@ -170,6 +170,6 @@ Classes representing internal objects :members: :no-undoc-members: -.. autoclass:: lammps.numpy::NumPyNeighList +.. autoclass:: lammps.numpy_wrapper::NumPyNeighList :members: :no-undoc-members: diff --git a/doc/src/Python_neighbor.rst b/doc/src/Python_neighbor.rst index 80651b608f..cba117ad20 100644 --- a/doc/src/Python_neighbor.rst +++ b/doc/src/Python_neighbor.rst @@ -14,5 +14,5 @@ Neighbor list access **NumPy Methods:** -* :py:meth:`lammps.numpy.get_neighlist() `: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays -* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() `: Get element in neighbor list and its neighbors (as numpy array) +* :py:meth:`lammps.numpy.get_neighlist() `: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays +* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() `: Get element in neighbor list and its neighbors (as numpy array) diff --git a/doc/src/Python_objects.rst b/doc/src/Python_objects.rst index ec29863d38..4c8161b8bd 100644 --- a/doc/src/Python_objects.rst +++ b/doc/src/Python_objects.rst @@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. Python subscripting. The values will be zero for atoms not in the specified group. - :py:meth:`lammps.numpy.extract_compute() `, - :py:meth:`lammps.numpy.extract_fix() `, and - :py:meth:`lammps.numpy.extract_variable() ` are + :py:meth:`lammps.numpy.extract_compute() `, + :py:meth:`lammps.numpy.extract_fix() `, and + :py:meth:`lammps.numpy.extract_variable() ` are equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers. The :py:meth:`lammps.set_variable() ` method sets an @@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module. **NumPy Methods**: - * :py:meth:`lammps.numpy.extract_compute() `: extract value(s) from a compute, return arrays as numpy arrays - * :py:meth:`lammps.numpy.extract_fix() `: extract value(s) from a fix, return arrays as numpy arrays - * :py:meth:`lammps.numpy.extract_variable() `: extract value(s) from a variable, return arrays as numpy arrays + * :py:meth:`lammps.numpy.extract_compute() `: extract value(s) from a compute, return arrays as numpy arrays + * :py:meth:`lammps.numpy.extract_fix() `: extract value(s) from a fix, return arrays as numpy arrays + * :py:meth:`lammps.numpy.extract_variable() `: extract value(s) from a variable, return arrays as numpy arrays .. tab:: PyLammps/IPyLammps API diff --git a/python/lammps/core.py b/python/lammps/core.py index d1bc7bc138..1a4650c285 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -1612,7 +1612,7 @@ class lammps(object): def get_neighlist(self, idx): """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index - See :py:meth:`lammps.numpy.get_neighlist() ` if you want to use + See :py:meth:`lammps.numpy.get_neighlist() ` if you want to use NumPy arrays instead of ``c_int`` pointers. :param idx: index of neighbor list