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GrupEstructuraElectronicaSimetria · Jun 7, 2021 · 4c4dd34 · 4c4dd34
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diff --git a/docs/conf.py b/docs/conf.py
@@ -52,7 +52,7 @@
 
 # General information about the project.
 project = u'cosymlib'
-copyright = u'2017, E. Bernuz, A. Carreras, M. Llunell & P. Alemany'
+copyright = u'2017-2021, 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

diff --git a/docs/cosym.rst b/docs/cosym.rst
diff --git a/docs/shape.rst b/docs/shape.rst
diff --git a/docs/shape_references.rst b/docs/shape_references.rst
@@ -40,11 +40,11 @@
 +         +------------+------------------------------------------------------------------+----------+
 |         | vT-2       |   Divacant tetrahedron (V-shape, 109.47°)                        |  |C2v|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | vOC-2      |   Tetravacant octahedron (L-shape, 90.47°)                       |  |C2v|   |
+|         | vOC-2      |   Tetravacant octahedron (L-shape, 90.00°)                       |  |C2v|   |
 +---------+------------+------------------------------------------------------------------+----------+
 |   3     | TP-3       |   Trigonal planar                                                |  |D3h|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | vT-3       |   Pyramid‡ (vacant tetrahedron)                                  |  |C3v|   |
+|         | vT-3       |   Pyramid\ :sup:`b`\  (vacant tetrahedron)                       |  |C3v|   |
 +         +------------+------------------------------------------------------------------+----------+
 |         | fac-vOC-3  |   fac-Trivacant octahedron                                       |  |C3v|   |
 +         +------------+------------------------------------------------------------------+----------+
@@ -54,17 +54,17 @@
 +         +------------+------------------------------------------------------------------+----------+
 |         | T-4        |   Tetrahedron                                                    |  |Td|    |
 +         +------------+------------------------------------------------------------------+----------+
-|         | SS-4       |   Seesaw or sawhorse ‡ (cis-divacant octahedron)                 |  |C2v|   |
+|         | SS-4       |   Seesaw or sawhorse\ :sup:`b`\  (cis-divacant octahedron)       |  |C2v|   |
 +         +------------+------------------------------------------------------------------+----------+
 |         | vTBPY-4    |   Axially vacant trigonal bipyramid                              |  |C3v|   |
 +---------+------------+------------------------------------------------------------------+----------+
 |   5     | PP-5       |   Pentagon                                                       |  |D5h|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | vOC-5      |   Vacant octahedron ‡ (Johnson square pyramid, J1)               |  |C4v|   |
+|         | vOC-5      |   Vacant octahedron\ :sup:`b`\  (Johnson square pyramid, J1)     |  |C4v|   |
 +         +------------+------------------------------------------------------------------+----------+
 |         | TBPY-5     |   Trigonal bipyramid                                             |  |D3h|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | SPY-5      |   Square pyramid §                                               |  |C4v|   |
+|         | SPY-5      |   Square pyramid\ :sup:`c`\                                      |  |C4v|   |
 +         +------------+------------------------------------------------------------------+----------+
 |         | JTBPY-5    |   Johnson trigonal bipyramid (J12)                               |  |D3h|   |
 +---------+------------+------------------------------------------------------------------+----------+
@@ -84,9 +84,9 @@
 +         +------------+------------------------------------------------------------------+----------+
 |         | PBPY-7     |   Pentagonal bipyramid                                           |  |D5h|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | COC-7      |   Capped octahedron *                                            |  |C3v|   |
+|         | COC-7      |   Capped octahedron\ :sup:`a`\                                   |  |C3v|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | CTPR-7     |   Capped trigonal prism *                                        |  |C2v|   |
+|         | CTPR-7     |   Capped trigonal prism\ :sup:`a`\                               |  |C2v|   |
 +         +------------+------------------------------------------------------------------+----------+
 |         | JPBPY-7    |   Johnson pentagonal bipyramid (J13)                             |  |D5h|   |
 +         +------------+------------------------------------------------------------------+----------+
@@ -164,7 +164,7 @@
 +         +------------+------------------------------------------------------------------+----------+
 |         | JSPC-10    |   Sphenocorona (J87)                                             |  |C2v|   |
 +         +------------+------------------------------------------------------------------+----------+
-|         | SDD-10     |   Staggered dodecahedron (2:6:2) #                               |  |D2|    |
+|         | SDD-10     |   Staggered dodecahedron (2:6:2)\ :sup:`e`\                      |  |D2|    |
 +         +------------+------------------------------------------------------------------+----------+
 |         | TD-10      |   Tetradecahedron (2:6:2)                                        |  |C2v|   |
 +         +------------+------------------------------------------------------------------+----------+
@@ -210,7 +210,7 @@
 +         +------------+------------------------------------------------------------------+----------+
 |         | JSPMC-12   |   Sphenomegacorona (J88)                                         |  |Cs|    |
 +---------+------------+------------------------------------------------------------------+----------+
-|   20    | DD-20      |   Dodecahedron †                                                 |  |Ih|    |
+|   20    | DD-20      |   Dodecahedron\ :sup:`d`\                                        |  |Ih|    |
 +---------+------------+------------------------------------------------------------------+----------+
 |   24    | TCU-24     |   Truncated cube                                                 |  |Oh|    |
 +         +------------+------------------------------------------------------------------+----------+
@@ -221,12 +221,12 @@
 |   60    | TRIC-60    |   Truncated icosahedron (fullerene)                              |  |Ih|    |
 +---------+------------+------------------------------------------------------------------+----------+
 
-| \* Non regular polyhedron, for definition of reference shape see references above.
-| ‡ A regular polyhedron with one or two vertices removed.
-| § Spherical distribution of vertices with mass center at the origin (apical-basal bond angles of 104.45°).
-| † For polyhedra with more than 12 vertices the calculation times may be unpractical, for now avoid this calculations
+| a Non regular polyhedron.
+| b  A regular polyhedron with one or two vertices removed.
+| c Spherical distribution of vertices with mass center at the origin (apical-basal bond angles of 104.45°).
+| d For polyhedra with more than 12 vertices the calculation times may be unpractical, for now avoid this calculations
     an upgrade is comming soon.
-| # This is a chiral polyhedron. It must be noticed that the algorithm used by Shape does not distinguish
+| e This is a chiral polyhedron. It must be noticed that the algorithm used by Shape does not distinguish
     the two enantiomers of a chiral shape. Therefore, whenever a chiral reference polyhedron is used, the resulting shape
     measures may not refer to that specific polyhedron but to its enantiomer.
 
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -76,7 +76,9 @@ included in the present distribution of **cosymlib**.
 
 General task scripts
 --------------------
-qqqqq
+
+In cosymlib library there several task scripts availables that can be run in a terminal as command lines. The following
+subsections describe the general usage of all of them.
 
 --------
 
@@ -603,35 +605,70 @@ available and list below. For more information of these commands go to gsym subs
 
 esym
 ^^^^^^
-qqqqq
+We are currenly working on this feature of the program regarding the electronic structure symmetry of molecules,
+therefore the actual script is under construction.
 
 --------
 
 cosym
 ^^^^^
-qqqqq
+This script is a general script that cover all the previous scripts.
 
 --------
 
 
 Specific task scripts
 ---------------------
 
-qqqqq
+In this section the specific task scripts are described.
 
 --------
 
 shape_map
 ^^^^^^^^^
-qqqqq
+The ``shape_map`` script calculate the continuous shape measures of a single or multiple structures with two reference
+structures in the same way the shape script does. However, it computes additional information like the minimum
+distortion pathway between the two reference structures, plus the deviation and the generalized coordinate of each
+user's structure.
+The most common commands available in the script are similar to the commands found in the shape script. The required
+commands are the ``-m_1 SH1` (or ``--measure_1``) and the ``-m_2 SH2`` flags, where SH1 and SH2 are the reference
+structure labels available in the program. Additionally, these flags can be substituted by the ``-m_custom_1 SH1`` or
+the ``-m_custom_2 SH2`` to indicate the program that SH1 and/or SH2 are the files containing a custom reference
+structure.
+Moreover, a set of flags are available to control the different plot options on the shape_map. The
+``--min_dev MIN_DEV`` and ``--max_dev MAX_DEV`` will only show the structures that are between the minimum and maximum
+deviation values (MIN_DEV and MAX_DEV), while the ``--min_gco MIN_GCO`` and ``--max_gco MAX_GCO`` show the structure
+that are at the MIN_GCO to MAX-GCO range of the generalized coordinate. In addition, the  user can plot more resolution
+minimal distortion pathways by setting the number of structures needed to compute the curve with the
+``--n_points N_POINTS`` flag.
+
+Finally, a set of mutual flags found in all scripts is available and listed below:
+
++-----------------+-----------------------+
+|    Short Flag   |   Explicit flag       |
++-----------------+-----------------------+
+|     ``-h``      |    ``--help``         |
++-----------------+-----------------------+
+|     ``-l``      |    ``--labels``       |
++-----------------+-----------------------+
+|     ``-o``      |    ``--output_name``  |
++-----------------+-----------------------+
+|     ``-c``      |    ``--central_atom`` |
++-----------------+-----------------------+
+|     ``-v``      |    ``--version``      |
++-----------------+-----------------------+
+
 
 --------
 
 Using cosymlib's APIs
 ---------------------
-qqqqq
+
+The current API's are under construction and a set of tutorials will be provide in a near future.
 
 Shape references
 ----------------
 
+Here are the available shape reference's labels and their symmetry that can be used by the shape program.
+
 .. include:: shape_references.rst