More moving stuff and things ...

parent 4608b54d
......@@ -133,7 +133,7 @@ def creates():
if line.startswith('# creates:'):
yield dirpath, filename, [file.rstrip(',')
for file in line.split()[2:]]
if 'build' in dirnames:
if 'build' in dirnames and dirpath == '.':
dirnames.remove('build')
......
......@@ -4,54 +4,6 @@
Builing things
==============
:func:`~ase.build.bulk`
:func:`~ase.build.surface`
:func:`~ase.build.molecule`
:func:`~ase.build.fcc100`
:func:`~ase.build.fcc110`
:func:`~ase.build.fcc111`
:func:`~ase.build.fcc211`
:func:`~ase.build.bcc100`
:func:`~ase.build.bcc110`
:func:`~ase.build.bcc111`
:func:`~ase.build.hcp0001`
:func:`~ase.build.hcp10m10`
:func:`~ase.build.diamond100`
:func:`~ase.build.diamond111`
:func:`~ase.build.fcc111_root`
:func:`~ase.build.bcc111_root`
:func:`~ase.build.hcp0001_root`
:func:`~ase.build.mx2`
:func:`~ase.build.add_adsorbate`
:func:`~ase.build.add_vacuum`
:func:`~ase.build.root_surface`
:func:`~ase.build.root_surface_analysis`
:func:`~ase.build.nanotube`
:func:`~ase.build.graphene_nanoribbon`
:func:`~ase.build.cut`
:func:`~ase.build.stack`
:func:`~ase.build.sort`
:func:`~ase.build.minimize_tilt`
:func:`~ase.build.niggli_reduce`
:func:`~ase.build.rotate`
:func:`~ase.build.minimize_rotation_and_translation`
.. toctree::
:maxdepth: 2
surface
ASE contains a number of modules for setting up atomic structures,
mainly molecules, bulk crystals and surfaces. Some of these modules
have overlapping functionality, but strike a different balance between
flexibility and ease-of-use.
**Common bulk crystals**
The :func:`ase.lattice.bulk` function can be used to create the most
......@@ -100,13 +52,61 @@ Some common molecules can be constructed using the
:func:`ase.build.molecule` function.
Read more: :ref:`molecular-data`.
:func:`~ase.build.bulk`
:func:`~ase.build.surface`
:func:`~ase.build.molecule`
.. list-table::
* - :func:`~ase.build.fcc100`
- :func:`~ase.build.fcc110`
- :func:`~ase.build.fcc111`
* - :func:`~ase.build.fcc211`
- :func:`~ase.build.bcc100`
- :func:`~ase.build.bcc110`
* - :func:`~ase.build.bcc111`
- :func:`~ase.build.hcp0001`
- :func:`~ase.build.hcp10m10`
* - :func:`~ase.build.diamond100`
- :func:`~ase.build.diamond111`
- :func:`~ase.build.fcc111_root`
* - :func:`~ase.build.bcc111_root`
- :func:`~ase.build.hcp0001_root`
- :func:`~ase.build.mx2`
* - :func:`~ase.build.add_adsorbate`
- :func:`~ase.build.add_vacuum`
- :func:`~ase.build.root_surface`
:func:`~ase.build.nanotube`
:func:`~ase.build.graphene_nanoribbon`
:func:`~ase.build.cut`
:func:`~ase.build.stack`
:func:`~ase.build.sort`
:func:`~ase.build.minimize_tilt`
:func:`~ase.build.niggli_reduce`
:func:`~ase.build.rotate`
:func:`~ase.build.minimize_rotation_and_translation`
.. seealso::
* The :mod:`ase.lattice` module
* The :mod:`~ase.spacegroup` module
* The :mod:`~ase.build` module
* The :mod:`ase.spacegroup` module
* The :mod:`ase.geometry` module
.. toctree::
:maxdepth: 2
surface
tools
Molecules
=========
......@@ -121,15 +121,16 @@ Example::
To see a list of available molecules in the default set, use::
>>> from ase.data.g2 import data
>>> data.viewkeys()
>>> from ase.collection import g2
>>> g2.names
.. _bulk-crystal-section:
Common bulk crystals
====================
.. autofunction:: ase.lattice.bulk
.. autofunction:: bulk
examples:
......@@ -195,3 +196,13 @@ examples:
.. |gnr1| image:: gnr1.png
.. |gnr2| image:: gnr2.png
ASE contains a number of modules for setting up atomic structures,
mainly molecules, bulk crystals and surfaces. Some of these modules
have overlapping functionality, but strike a different balance between
flexibility and ease-of-use.
.. _lattice-surface-section:
========
Surfaces
========
.. module:: ase.build
.. currentmodule:: ase.build
Common surfaces
===============
......@@ -17,7 +14,6 @@ the modules described in the section :ref:`general-crystal-section`, but these
utility functions make common tasks easier.
Example
-------
......@@ -99,7 +95,7 @@ later be used when adding an adsorbate with
The following functions are provided
````````````````````````````````````
.. function:: fcc100(symbol, size, a=None, vacuum=0.0)
.. autofunction:: fcc100
.. function:: fcc110(symbol, size, a=None, vacuum=0.0)
.. function:: bcc100(symbol, size, a=None, vacuum=0.0)
.. function:: hcp10m10(symbol, size, a=None, c=None, vacuum=0.0)
......@@ -223,8 +219,6 @@ also possible to add one or more adsorbates.
Create specific non-common surfaces
===================================
.. versionadded:: 3.5.2
In addition to the most normal surfaces, a function has been
constructed to create more uncommon surfaces that one could be
interested in. It is constructed upon the Miller Indices defining the
......
=========================
Tools for building things
=========================
.. autofunction:: ase.build.cut
.. autofunction:: ase.build.stack
.. autofunction:: ase.build.sort
.. autofunction:: ase.build.rotate
.. autofunction:: ase.build.niggli_reduce
.. autofunction:: ase.build.minimize_tilt
.. autofunction:: ase.build.minimize_rotation_and_translation
......@@ -6,6 +6,14 @@
File input and output
=====================
.. seealso::
* :ref:`trajectory`
.. toctree::
trajectory
The :mod:`ase.io` module has three basic functions: :func:`read`,
:func:`iread` and :func:`write`. The methods are described here:
......
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