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Fix docs after PR #2592

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This commit is contained in:
Richard Berger
2021-02-15 13:19:25 -05:00
parent 16004e8f45
commit d256614c9f
5 changed files with 16 additions and 16 deletions
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2
doc/src/Python_atoms.rst
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@ -50,7 +50,7 @@ against invalid accesses.
**Numpy Methods**: **Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
.. tab:: PyLammps/IPyLammps API .. tab:: PyLammps/IPyLammps API

12
doc/src/Python_module.rst
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@ -61,7 +61,7 @@ functions. Below is a detailed documentation of the API.
.. autoclass:: lammps.lammps .. autoclass:: lammps.lammps
:members: :members:
.. autoclass:: lammps.numpy::numpy_wrapper .. autoclass:: lammps.numpy_wrapper::numpy_wrapper
:members: :members:
---------- ----------
@ -134,8 +134,8 @@ Style Constants
to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST` to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
for the equivalent constants in the C library interface. Used in 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.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`. :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_type_constants: .. _py_type_constants:
@ -149,8 +149,8 @@ Type Constants
to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST` to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST`
for the equivalent constants in the C library interface. Used in 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.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`. :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_vartype_constants: .. _py_vartype_constants:
@ -170,6 +170,6 @@ Classes representing internal objects
:members: :members:
:no-undoc-members: :no-undoc-members:
.. autoclass:: lammps.numpy::NumPyNeighList .. autoclass:: lammps.numpy_wrapper::NumPyNeighList
:members: :members:
:no-undoc-members: :no-undoc-members:

4
doc/src/Python_neighbor.rst
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@ -14,5 +14,5 @@ Neighbor list access
**NumPy Methods:** **NumPy Methods:**
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays * :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.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() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array) * :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

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doc/src/Python_objects.rst
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@ -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 Python subscripting. The values will be zero for atoms not in the
specified group. specified group.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`, :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers. equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
**NumPy Methods**: **NumPy Methods**:
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays * :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays * :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays * :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API .. tab:: PyLammps/IPyLammps API

2
python/lammps/core.py
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@ -1612,7 +1612,7 @@ class lammps(object):
def get_neighlist(self, idx): def get_neighlist(self, idx):
"""Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index
See :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>` if you want to use See :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>` if you want to use
NumPy arrays instead of ``c_int`` pointers. NumPy arrays instead of ``c_int`` pointers.
:param idx: index of neighbor list :param idx: index of neighbor list