Update manual

GrupEstructuraElectronicaSimetria · Dec 21, 2020 · d1c6a4f · d1c6a4f
1 parent 2868f7b
commit d1c6a4f
Show file tree

Hide file tree

Showing 25 changed files with 67 additions and 28 deletions.
diff --git a/cosymlib/shape/__init__.py b/cosymlib/shape/__init__.py
@@ -20,8 +20,14 @@ def _get_key(central_atom, reference, fix_permutation=False, reference_2=''):
 
 
 class Shape:
+    """
+    Shape class
+
+    :param geometry:
+    """
     def __init__(self, geometry):
 
+
         # Allow geometry or molecule to be imported instead of crude Cartesian coordinates
         try:
             self._coordinates = geometry.get_positions()
@@ -39,6 +45,7 @@ def __init__(self, geometry):
         self._path_deviation = {}
         self._gen_coord = {}
 
+
     # Function description
     def measure(self, reference, central_atom=0, fix_permutation=False):
         key = _get_key(central_atom, reference, fix_permutation=fix_permutation)

diff --git a/cosymlib/symmetry/__init__.py b/cosymlib/symmetry/__init__.py
@@ -25,6 +25,18 @@ def _get_key_wfnsym(group, vector_axis1, vector_axis2, center, alpha_occupancy,
 
 
 class Symmetry:
+    """
+    Symmetry class
+
+    :param structure:
+    :param central_atom:
+    :param center:
+    :param connect_thresh:
+    :param multi:
+    :param axis:
+    :param axis2:
+    """
+
     def __init__(self,
                  structure,
                  central_atom=0,

diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,16 @@
+API Reference
+=============
+.. automodule:: cosymlib
+    :members: Cosymlib
+
+Symmetry
+--------
+.. automodule:: cosymlib.symmetry
+    :members: Symmetry
+
+
+Shape
+-----
+.. automodule:: cosymlib.shape
+    :members: Shape
+
diff --git a/docs/conf.py b/docs/conf.py
@@ -31,10 +31,10 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages']
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.githubpages']
 
 
 # Add any paths that contain templates here, relative to this directory.
@@ -51,8 +51,8 @@
 
 # General information about the project.
 project = u'cosymlib'
-copyright = u'2017, Efrem & Abel'
-author = u'Efrem & Abel'
+copyright = u'2017, E. Bernuz, A. Carreras, M. Llunell & P. Alemany'
+author = u'E. Bernuz, A. Carreras, M. Llunell & P. Alemany'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -82,7 +82,7 @@
 todo_include_todos = False
 
 
-autodoc_mock_imports = ['cosymlib.molecule']
+autodoc_mock_imports = ['cosymlib.molecule, cosymlib.shape', 'wfnsympy', 'symgroupy']
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -152,7 +152,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'cosymlib.tex', u'cosymlib Documentation',
-     u'Efrem \\& Abel', 'manual'),
+     u'E. Bernuz, A. Carreras, M. Llunell & P. Alemany', 'manual'),
 ]
 
 

diff --git a/docs/cosym.rst b/docs/cosym.rst
@@ -4,7 +4,7 @@
 Executing program
 =================
 
-This script run symeess from terminal
+This script run cosymlib from terminal
 
 .. module:: scripts/cosym
 

diff --git a/docs/User_Manual_SHAPE_v2.1.pdf → docs/downloads/manual_shape_2_1.pdf b/docs/User_Manual_SHAPE_v2.1.pdf → docs/downloads/manual_shape_2_1.pdf
diff --git a/docs/2016_iqtcub_retallat.png → docs/images/2016_iqtcub_retallat.png b/docs/2016_iqtcub_retallat.png → docs/images/2016_iqtcub_retallat.png
diff --git a/docs/CCM_def.png → docs/images/CCM_def.png b/docs/CCM_def.png → docs/images/CCM_def.png
diff --git a/docs/CSM_def.png → docs/images/CSM_def.png b/docs/CSM_def.png → docs/images/CSM_def.png
diff --git a/docs/CSM_eq.png → docs/images/CSM_eq.png b/docs/CSM_eq.png → docs/images/CSM_eq.png
diff --git a/docs/CShM_def.png → docs/images/CShM_def.png b/docs/CShM_def.png → docs/images/CShM_def.png
diff --git a/docs/CShM_eq.png → docs/images/CShM_eq.png b/docs/CShM_eq.png → docs/images/CShM_eq.png
diff --git a/docs/QCSM_eq.png → docs/images/QCSM_eq.png b/docs/QCSM_eq.png → docs/images/QCSM_eq.png
diff --git a/docs/QCSM_example.png → docs/images/QCSM_example.png b/docs/QCSM_example.png → docs/images/QCSM_example.png
diff --git a/docs/logo-ess.tiff → docs/images/logo-ess.tiff b/docs/logo-ess.tiff → docs/images/logo-ess.tiff
diff --git a/docs/logo_iqtc.png → docs/images/logo_iqtc.png b/docs/logo_iqtc.png → docs/images/logo_iqtc.png
diff --git a/docs/logo_mmaeztu.png → docs/images/logo_mmaeztu.png b/docs/logo_mmaeztu.png → docs/images/logo_mmaeztu.png
diff --git a/docs/logo_ub.jpg → docs/images/logo_ub.jpg b/docs/logo_ub.jpg → docs/images/logo_ub.jpg
diff --git a/docs/ml8.png → docs/images/ml8.png b/docs/ml8.png → docs/images/ml8.png
diff --git a/docs/quadr.png → docs/images/quadr.png b/docs/quadr.png → docs/images/quadr.png
diff --git a/docs/soev_eq.png → docs/images/soev_eq.png b/docs/soev_eq.png → docs/images/soev_eq.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,6 +1,6 @@
 .. highlight:: rst
 
-.. image:: ml8.png
+.. image:: images/ml8.png
     :height: 80px
     :align: left
 
@@ -39,26 +39,27 @@ The basic tasks included in the current version of **cosymlib** are:
     usage
     tutorials
     links
+    api
 
 **Cosymlib** is being developed by the **Electronic Structure & Symmetry (ESS)** group
 at the Department de Ciència de Material i Química Física
 and the Institut de Química Teòrica i Computacional (IQTCUB). University of Barcelona.
 
 ------
 
-.. image:: logo-ess.tiff
+.. image:: images/logo-ess.tiff
     :height: 52px
     :align: left
 
-.. image:: logo_ub.jpg
+.. image:: images/logo_ub.jpg
     :height: 52px
     :align: left
 
-.. image:: logo_iqtc.png
+.. image:: images/logo_iqtc.png
     :height: 52px
     :align: left
 
-.. image:: logo_mmaeztu.png
+.. image:: images/logo_mmaeztu.png
     :height: 52px
     :align: left
 

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -36,7 +36,7 @@ In a nutshell, the continuous shape measure S\ :sub:`P`\ (Q) of object Q with re
 reference shape P is an indicator of how much Q resembles another object P\ :sub:`0`\  with a given
 ideal shape, for instance a square as in the figure below.
 
-.. image:: CShM_def.png
+.. image:: images/CShM_def.png
     :height: 160px
     :align: center
 
@@ -48,7 +48,7 @@ Q and P, where P is the image of P\ :sub:`0`\  after these transformations.
 If both the problem and the reference structures Q and P are defined as a set of vertices, we can
 define the shape measure simply as:
 
-.. image:: CShM_eq.png
+.. image:: images/CShM_eq.png
     :height: 105px
     :align: center
 
@@ -100,7 +100,7 @@ with respect to a given point symmetry group G, denoted as S\ :sub:`G`\ (Q), yie
 totally analogous to the equation above, in which Q refers again to the problem structure,
 but where P is now the G-symmetric structure closest to Q:
 
-.. image:: CSM_eq.png
+.. image:: images/CSM_eq.png
     :height: 90px
     :align: center
 
@@ -118,7 +118,7 @@ optimal overlap of our quadrangle Q with a particular rectangle P as in a shape
 to consider also which is the ratio between the side lengths of best matching rectangle and
 optimize also with respect to this parameter.
 
-.. image:: CSM_def.png
+.. image:: images/CSM_def.png
     :height: 180px
     :align: center
 
@@ -167,7 +167,7 @@ prominent role in chemistry. A chiral object is usually described as an object t
 superposed with its mirror image. In this sense, we could obtain a continuous chirality measure
 by using the same equation as for shape measures just by replacing P by the mirror image of Q.
 
-.. image:: CCM_def.png
+.. image:: images/CCM_def.png
     :height: 150px
     :align: center
 
@@ -208,7 +208,7 @@ continuous symmetry and shape measures to more complex objects that cannot be si
 by a set of vertices such as matrices or functions. In this case the definition of the continuous
 symmetry measure is:
 
-.. image:: QCSM_eq.png
+.. image:: images/QCSM_eq.png
     :height: 60px
     :align: center
 
@@ -220,7 +220,7 @@ h symmetry operations g\ :sub:`i`\  that form group G. The precise definition on
 overlaps depends, of course, on the nature of the object Q. For molecular orbitals as obtained in
 a quantum chemical calculation we have:
 
-.. image:: soev_eq.png
+.. image:: images/soev_eq.png
     :height: 40px
     :align: center
 
@@ -230,7 +230,7 @@ wavefunction) by the whole electron density. Using this type of symmetry measure
 to compare the symmetry contents of the electronic structure of molecules, for instance by comparing
 the inversion symmetry measure for different diatomic molecules as in the example below:
 
-.. image:: QCSM_example.png
+.. image:: images/QCSM_example.png
     :height: 150px
     :align: center
 

diff --git a/docs/shape.rst b/docs/shape.rst
@@ -9,7 +9,7 @@ This is the shape module
 
   shape_references
 
-.. automodule:: symeess.shape
+.. automodule:: cosymlib.shape
    :members:
    :show-inheritance:
 

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -109,6 +109,7 @@ x, y, z for each atom (vertex) in the structure.
 ``fname.xyz`` files read by shape may contain a single structure as in the previous example or
 multiple structures (all with the same number of atoms), in which case a block:
 ::
+
     Title
     label1 x  y  z
      ...
@@ -124,6 +125,7 @@ file formats)*.
 The basic call to the shape script must provide the the file containing the input structure and the
 reference shape with respect to which the shape measure is calculated.
 ::
+
    $ shape input_file -m SH
 
 where ``input_file`` is a file containing the structural information in a valid format, for instance
@@ -241,6 +243,7 @@ Using
 
 we find:
 ::
+
     Available reference structures with 7 Vertices:
 
     Label       Sym       Info
@@ -268,6 +271,7 @@ Note also that, as shown in this example, the position of the ``-c N``  and
 ``-m OC-6`` flags, or the ``input_file`` in the call to the shape script is totally irrelevant
 and any combination such as:
 ::
+
     $ shape cocl6.xyz -c 1 -m OC-6
 
     $ shape  -c 1 -m OC-6 cocl6.xyz
@@ -285,6 +289,7 @@ call.
 Let us consider a ``struct.xyz`` file containing the geometry for an approximately square
 H\ :sub:`4`\  molecule.
 ::
+
     4
     H4 Quadrangle
     H    1.1   0.9  0.0
@@ -300,6 +305,7 @@ is the closest square to its actual distorted structure we may use:
 
 which will yield:
 ::
+
     Starting...
     ----------------------------------------------------------------------
      COSYM v0.7.4
@@ -329,7 +335,7 @@ with the coordinates of the problem structure and its closest ideal (square)
 structure, which we can use to plot the superposition of problem structure (in red)
 and the ideal reference (in blue):
 
-.. image:: quadr.png
+.. image:: images/quadr.png
     :height: 220 px
     :align: center
 
@@ -435,7 +441,7 @@ our previous ``SHAPE`` program.  Follow the link below  for a pdf version of the
 SHAPE ver. 2.1 where you will find all information to perform a continuous shape analysis using
 this option.
 
-:download: `SHAPE ver. 2.1 User's guide.  <User_Manual_SHAPE_v2.1.pdf>`_
+:download:`SHAPE ver. 2.1 User's guide <downloads/manual_shape_2_1.pdf>`
 
 
 
@@ -481,10 +487,7 @@ qqqqq
 
 Using cosymlib's APIs
 ---------------------
-
 qqqqq
 
---------
-