Add NAMD IDWS dataset

docs/namd.rst

@@ -15,9 +15,16 @@ engine. They can be accessed using the following accessor functions:
 .. autosummary::
 
    load_tyr2ala
+   load_idws
 
 .. _namd_tyr2ala:
 
 .. include:: ../src/alchemtest/namd/tyr2ala/descr.rst
 
 .. autofunction:: alchemtest.namd.load_tyr2ala
+
+.. _namd_idws:
+
+.. include:: ../src/alchemtest/namd/idws/descr.rst
+
+.. autofunction:: alchemtest.namd.load_idws

src/alchemtest/namd/__init__.py

@@ -3,3 +3,4 @@
 """
 
 from .access import load_tyr2ala
+from .access import load_idws

src/alchemtest/namd/access.py

@@ -30,3 +30,24 @@ def load_tyr2ala():
     return Bunch(data=data,
                  DESCR=fdescr)
 
+def load_idws():
+    """Load the NAMD IDWS dataset.
+
+    Returns
+    -------
+    data : Bunch
+        Dictionary-like object, the interesting attributes are:
+
+        - 'data' : the data files by alchemical leg
+        - 'DESCR': the full description of the dataset
+
+    """
+
+    module_path = dirname(__file__)
+    data = {'forward': [join(module_path, 'idws', 'quickidws.fepout.bz2']}
+
+    with open(join(module_path, 'idws', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)

src/alchemtest/namd/idws/descr.rst

@@ -0,0 +1,33 @@
+NAMD: free energy of dummy ethane to ethane "mutation" in aqueous solution
+==========================================================================
+
+Free energy change from mutating an ethane molecule into an ethane molecule, 
+turning a H atom into a methyl group and conversely.
+Expected free energy is zero, however the dataset is tiny (sufficient for
+testing purposes).
+Uses Interleaved Double-Wide Sampling (Hénin and Brannigan).
+
+Notes
+-----
+Data Set Characteristics:
+    :Number of Legs: 1 (forward mutation in water with IDWS sampling)
+    :Number of Windows: 11
+    :Length of Windows: 500 fs (each window interspersed with 100 fs equilibration)
+    :System Size: 1030 atoms
+    :Temperature: 300 K
+    :Pressure: 1 bar
+    :Alchemical Pathway: dummy mutation of ethane into ethane using dual topology
+                         hybrid molecule. Nonbonded interactions of perturbed
+                         atoms are scaled with their environment.
+    :Theoretical Free Energy difference: 0
+    :Missing Values: None
+    :Energy unit: kcal/mol
+    :Time unit: step
+    :Date: May 2021
+    :Donor: J Hénin
+    :License: `CC0 <https://creativecommons.org/publicdomain/zero/1.0/>`_
+              Public Domain Dedication
+
+This dataset was generated using the `NAMD
+<http://http://www.ks.uiuc.edu/Research/namd/>`_ molecular dynamics
+engine.