expanded the documenatation

README.md

@@ -3,51 +3,6 @@ pysisphus implements Chain Of States (COS) methods like Nudged Elastic Band (NEB
 
 **This software is still work in progress and shouldn't be used for production runs. Use at your own risk.**
 
-## Dependencies
-
-	python3.6+
-	scipy
-	numpy
-	matplotlib
-	pytest
-	natsort
-	pyyaml
-
-Usage of pysisyphus within the **anaconda** distribution is recommended.
-
-## Installation
-### Install the code
-The **recommended way**, as the version on pypi may be outdated:
-
-    cd [root dir where you want to keep pysisyphus]
-	git clone https://github.com/eljost/pysisyphus
-	cd pysisyphus
-	python setup.py develop
-
-or **(not recommended)**:
-
-	pip install pysisyphus
-
-### Tell pysisyphus how to call your calculators	
-Create a file called `.pysisyphusrc` in your $HOME-directory containing the commands the call your installed calculators, e.g.:
-
-    [orca]
-    cmd=/scratch/programme/orca-4.0.1.2/orca
-
-    [xtb]
-    cmd=xtb
-
-    [openmolcas]
-    cmd=pymolcas
-
-    [gaussian09]
-    cmd=/usr/local/gaussian/g09/g09
-
-    [wfoverlap]
-    cmd=/scratch/wfoverlap_1.0/bin/wfoverlap.x
-
-When the specified path is not absolute but relative (as in the example config for xtb and openmolcas) the corresponding binaries have to be available on the $PATH! The **Turbomole** binaries are hardcoded and don't have to be specified here. 
-
 ## Usage
 pysisyphus provides three hooks that can be called from the shell (command line). The available commandas can be queried with the `-h` or `--help` arguments:
 

docs/api/pysisyphus.calculators.rst

@@ -0,0 +1,174 @@
+pysisyphus.calculators package
+==============================
+
+Submodules
+----------
+
+pysisyphus.calculators.AnaPot module
+------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPot2 module
+-------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPot2
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPot2D module
+--------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPot2D
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPot3 module
+-------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPot3
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPot4 module
+-------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPot4
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPotBase module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPotBase
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.AnaPotBase2D module
+------------------------------------------
+
+.. automodule:: pysisyphus.calculators.AnaPotBase2D
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.Calculator module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.Calculator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.Gaussian09 module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.Gaussian09
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.Gaussian16 module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.Gaussian16
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.IDPP module
+----------------------------------
+
+.. automodule:: pysisyphus.calculators.IDPP
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.MullerBrownPot module
+--------------------------------------------
+
+.. automodule:: pysisyphus.calculators.MullerBrownPot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.MullerBrownSympyPot module
+-------------------------------------------------
+
+.. automodule:: pysisyphus.calculators.MullerBrownSympyPot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.MullerBrownSympyPot2D module
+---------------------------------------------------
+
+.. automodule:: pysisyphus.calculators.MullerBrownSympyPot2D
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.ORCA module
+----------------------------------
+
+.. automodule:: pysisyphus.calculators.ORCA
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.OpenMolcas module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.OpenMolcas
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.Turbomole module
+---------------------------------------
+
+.. automodule:: pysisyphus.calculators.Turbomole
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.WFOWrapper module
+----------------------------------------
+
+.. automodule:: pysisyphus.calculators.WFOWrapper
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.XTB module
+---------------------------------
+
+.. automodule:: pysisyphus.calculators.XTB
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.calculators.parser module
+------------------------------------
+
+.. automodule:: pysisyphus.calculators.parser
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pysisyphus.calculators
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/pysisyphus.cos.rst

@@ -0,0 +1,54 @@
+pysisyphus.cos package
+======================
+
+Submodules
+----------
+
+pysisyphus.cos.ChainOfStates module
+-----------------------------------
+
+.. automodule:: pysisyphus.cos.ChainOfStates
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.cos.NEB module
+-------------------------
+
+.. automodule:: pysisyphus.cos.NEB
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.cos.NoSpringNeb module
+---------------------------------
+
+.. automodule:: pysisyphus.cos.NoSpringNeb
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.cos.OldTangentChainOfStates module
+---------------------------------------------
+
+.. automodule:: pysisyphus.cos.OldTangentChainOfStates
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.cos.SimpleZTS module
+-------------------------------
+
+.. automodule:: pysisyphus.cos.SimpleZTS
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pysisyphus.cos
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/api/pysisyphus.irc.rst

@@ -0,0 +1,78 @@
+pysisyphus.irc package
+======================
+
+Submodules
+----------
+
+pysisyphus.irc.DampedVelocityVerlet module
+------------------------------------------
+
+.. automodule:: pysisyphus.irc.DampedVelocityVerlet
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.Euler module
+---------------------------
+
+.. automodule:: pysisyphus.irc.Euler
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.GonzalesSchlegel module
+--------------------------------------
+
+.. automodule:: pysisyphus.irc.GonzalesSchlegel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.GonzalesSchlegelFail module
+------------------------------------------
+
+.. automodule:: pysisyphus.irc.GonzalesSchlegelFail
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.IMKMod module
+----------------------------
+
+.. automodule:: pysisyphus.irc.IMKMod
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.IRC module
+-------------------------
+
+.. automodule:: pysisyphus.irc.IRC
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.ParamPlot module
+-------------------------------
+
+.. automodule:: pysisyphus.irc.ParamPlot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pysisyphus.irc.PlotAnaPot module
+--------------------------------
+
+.. automodule:: pysisyphus.irc.PlotAnaPot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pysisyphus.irc
+    :members:
+    :undoc-members:
+    :show-inheritance: