Add NAMD test set that contains restarts (#55)

* Add scaffolding for NAMD restarted IDWS fepout test (see alchemistry/alchemlyb#135 )
* Add dataset for NAMD FEP run that was restarted a few times
* Add test
* Add entry for restarted dataset to docs/namd.rst

docs/namd.rst

@@ -28,3 +28,9 @@ engine. They can be accessed using the following accessor functions:
 .. include:: ../src/alchemtest/namd/idws/descr.rst
 
 .. autofunction:: alchemtest.namd.load_idws
+
+.. _namd_restarted:
+
+.. include:: ../src/alchemtest/namd/restarted/descr.rst
+
+.. autofunction:: alchemtest.namd.load_restarted

src/alchemtest/namd/__init__.py

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

src/alchemtest/namd/access.py

@@ -51,3 +51,25 @@ def load_idws():
 
     return Bunch(data=data,
                  DESCR=fdescr)
+
+def load_restarted():
+    """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 = {'both': glob(join(module_path, 'restarted', 'restarted*.fepout.bz2'))}
+
+    with open(join(module_path, 'restarted', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)

src/alchemtest/namd/restarted/descr.rst

@@ -0,0 +1,34 @@
+NAMD: free energy of tyrosine to alanine in vacuo
+=================================================
+
+Free energy change from mutating a Tyr into Ala in vacuo.
+Uses Interleaved Double-Wide Sampling (Hénin and Brannigan).
+Each lambda window was run separately, and NAMD was interrupted
+and restarted multiple times, such that one window may span
+multiple fepout files.
+
+Derived from NAMD FEP Tutorial, available at:
+https://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/
+
+Notes
+-----
+Data Set Characteristics:
+    :Number of Legs: 1 (forward mutation with IDWS sampling)
+    :Number of Windows: 11
+    :Length of Windows: 50 ps
+    :System Size: 57 atoms
+    :Temperature: 300 K
+    :Alchemical Pathway: Mutation of Tyr into Ala using hybrid molecule.
+                         Nonbonded interactions of perturbed atoms are scaled
+                         with their environment.
+    :Missing Values: None
+    :Energy unit: kcal/mol
+    :Time unit: step
+    :Date: August 2021
+    :Donor: Thomas T. Joseph
+    :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.

src/alchemtest/tests/test_namd.py

@@ -1,7 +1,7 @@
 '''Tests for all the NAMD datasets'''
 import pytest
 
-from alchemtest.namd import load_tyr2ala, load_idws
+from alchemtest.namd import load_tyr2ala, load_idws, load_restarted
 
 from . import BaseDatasetTest
 
@@ -10,6 +10,7 @@ class TestNAMD(BaseDatasetTest):
     @pytest.fixture(scope="class",
                     params = [(load_tyr2ala, ('forward', 'backward'), (1, 1)),
                               (load_idws, ('forward', ), (2,)),
+                              (load_restarted, ('both', ), (15,))
                               ])
     def dataset(self, request):
         return super(TestNAMD, self).dataset(request)