Adding GOMC free energy data sets (#34)

* Add GOMC data sets (for alchemistry/alchemlyb#78)
* update the documentation
* Change the file formatting. Store the all free energy files in inWater directory instead of storing in separate VDW and Coulomb directory.
* compress the free energy files
* close #33

docs/gomc.rst

@@ -0,0 +1,32 @@
+.. _gomc-datasets:
+
+===============
+GOMC datasets
+===============
+.. automodule:: alchemtest.gomc
+
+The :mod:`alchemlyb.gomc` module features datasets generated using the
+GPU Optimized Monte Carlo (`GOMC <http://gomc.eng.wayne.edu/>`_) simulation 
+engine. They can be accessed using the following accessor functions:
+
+.. currentmodule:: alchemtest.gomc
+
+.. autosummary::
+
+   load_benzene
+
+
+------------------
+Simple TI and FEP
+------------------
+
+The data sets contain derivatives of the Hamiltonian (TI) and free
+energy perturbation (FEP) data suitable for processing with FEP
+estimators as well as BAR/MBAR. Individual :math:`\lambda` windows
+were run independently.
+
+
+.. _gomc_benzene:
+.. include:: ../src/alchemtest/gomc/benzene/descr.rst
+
+.. autofunction:: alchemtest.gomc.load_benzene

docs/index.rst

@@ -58,4 +58,5 @@ of pull requests are very welcome.
     gmx
     amber
     namd
+    gomc
 

src/alchemtest/gomc/__init__.py

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+"""GOMC Monte Carlo simulation datasets.
+
+"""
+
+from .access import load_benzene

src/alchemtest/gomc/access.py

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+"""Accessors for GOMC datasets.
+
+"""
+
+from os.path import dirname, join
+from glob import glob
+
+from .. import Bunch
+
+def load_benzene():
+    """Load the GOMC benzene 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 = sorted(glob(join(module_path, 'benzene', 'inWater', 'Free_Energy_BOX_0_PRODUCTION_*.dat')))
+
+    with open(join(module_path, 'benzene', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)
+

src/alchemtest/gomc/benzene/descr.rst

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+GOMC: Benzene in water
+=========================
+
+Hydration free energy of benzene using `TraPPE-EH <https://pubs.acs.org/doi/10.1021/jp073586l>`_ 
+model and SPC water model.
+
+Notes
+-----
+Data Set Characteristics:
+    :Number of Legs: 2 (Coulomb, VDW)
+    :Number of Windows: 7 for Coulomb, 15 for VDW
+    :Length of Windows: 50 million Monte Carlo steps
+    :System Size: 1001 molecules
+    :Temperature: 298 K
+    :Pressure: 1 bar
+    :Alchemical Pathway: vacuum --> vdw --> vdw + coul
+    :Experimental Hydration Free Energy: -0.90 +- 0.2 kcal/mol
+    :Missing Values: None
+    :Energy unit: kJ/mol
+    :Time unit: Monte Carlo steps
+    :Creator: \M. Soroush Barhaghi
+    :Donor: Mohammad Soroush Barhaghi ([email protected])
+    :Date: July 2019
+    :License: `CC0
+	      <https://creativecommons.org/publicdomain/zero/1.0/>`_
+	      Public Domain Dedication       
+
+This dataset was generated using `GOMC <http://gomc.eng.wayne.edu/>`_ Monte Carlo simulation engine. 
+
+Experimental value sourced from [Mobley2013]_.
+
+.. [Mobley2013] Mobley, David L. (2013). Experimental and Calculated Small 
+    Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical 
+    Sciences, UCI. Retrieved from: http://escholarship.org/uc/item/6sd403pz