Lammps (#96)

* Lammps test draft

* Update docs

* Add data

* Update docs appropriately

* Update file names

* Add lj_dimer

* Add tests lj dimer

* Add midas doi

* Adjust language in sphinx

* Fix doc conf.py intersphinx_mapping

* Fix docs

* Compress files

.gitignore

@@ -3,6 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# VS Code
+.vscode
+
 # C extensions
 *.so
 
@@ -107,5 +110,5 @@ ENV/
 
 # In-tree generated files
 */_version.py
-*/.DS_Store
+*.DS_Store
 */.idea/

alchemtest/lammps/__init__.py

@@ -0,0 +1,5 @@
+"""Simulation datasets in any form.
+
+"""
+
+from .access import load_benzene, load_lj_dimer

alchemtest/lammps/access.py

@@ -0,0 +1,75 @@
+"""LAMMPS datasets.
+
+"""
+
+from os.path import dirname, join
+from glob import glob
+
+from .. import Bunch
+
+def load_benzene():
+    """Load data set of benzene in water.
+
+    Returns
+    -------
+    data: Bunch
+        Dictionary-like object, the interesting attributes are:
+
+        - 'data' : the data files from lammps dump output
+        
+            * "mbar": Files formatted for BAR or MBAR
+            
+                * '1_coul-off': NPT removal of benzene's charges
+                * '2_vdw': NPT decoupling of vdw forces between benzene and water
+                * '3_coul-on': NVT in vacuum restoration of benzene's charges
+                
+            * "ti"
+            
+                * '1_coul-off': NPT removal of benzene's charges
+                * '2_vdw': NPT decoupling of vdw forces between benzene and water
+                * '3_coul-on': NVT in vacuum restoration of benzene's charges
+        
+        - 'DESCR': the full description of the dataset
+
+    """
+    module_path = dirname(__file__)
+    data = {
+        "mbar": {
+            '1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/mbar*.txt.bz2')),
+            '2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/mbar*.txt.bz2')),
+            '3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/mbar*.txt.bz2')),                
+        },
+        "ti": {
+            '1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/ti*.txt.bz2')),
+            '2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/ti*.txt.bz2')),
+            '3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/ti*.txt.bz2')),    
+        }
+    }
+
+    with open(join(module_path, 'benzene', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)
+
+
+def load_lj_dimer():
+    """Load data set of LJ dimer in solvent.
+
+    Returns
+    -------
+    data: Bunch
+        Dictionary-like object, the interesting attributes are:
+
+        - 'data' : the data files from lammps dump output        
+        - 'DESCR': the full description of the dataset
+
+    """
+    module_path = dirname(__file__)
+    data = glob(join(module_path, 'lj_dimer/cross_epsilon/linear*.txt.bz2'))
+
+    with open(join(module_path, 'lj_dimer', 'descr.rst')) as rst_file:
+        fdescr = rst_file.read()
+
+    return Bunch(data=data,
+                 DESCR=fdescr)