Merge branch 'master' of git@github.com:eurydyce/MDANSE.git

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -40,12 +40,12 @@ from MDANSE.MolecularDynamics.Trajectory import read_atoms_trajectory
 
 class AngularCorrelation(IJob):
     '''
-    Computes the angular correlation for a set of molecules.
+    Computes the angular correlation for a vector defined with respect to a molecule or set of molecules.
     
-    Vector defined by user, starting at the origin pointing towards the direction.
-    Origin and direction can either be an atom or a center definition. In this particular case the origin
-    is the head group geometric center designated with the sphere and the direction is simply the last atom
-    of the tail chain. The correlation is calculated for the angle formed between the same vector at 
+    Vector defined by user, starting at the origin pointing in a particular direction.
+    Origin and direction can either be an atom or a centre definition (centre of a group of atoms). For example, the origin
+    could be defined by the geometric centre of the head group of a surfactant molecule and the direction simply by the last atom
+    of the tail or chain. The correlation is calculated for the angle formed by the same vector at 
     different times
 
     **Calculation:** \n

MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -44,8 +44,9 @@ class AreaPerMolecule(IJob):
     '''
     Computes the area per molecule.
     
-    The area per molecule is computed by simply dividing the surface of one of the simulation box face (ab, bc or ac) by the
-    number of molecule with a given name. This property should be a constant unless the simulation performed was in NPT ensemble.
+    The area per molecule is computed by simply dividing the surface of one of the simulation box faces (ab, bc or ac) by the
+    number of molecules with a given name. This property should be a constant unless the simulation performed was in the NPT ensemble.
+	This analysis is relevant for oriented structures like lipid membranes.
     '''
     
     type = 'apm'

MDANSE/Framework/Jobs/BoxTranslatedTrajectory.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -44,7 +44,7 @@ from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 
 class BoxCenteredTrajectory(IJob):
     """
-    Build a new trajectory by translating a given atom selection on the center of the simulation box. 
+    Build a new trajectory by translating the contents of the simulation box such that a given atom selection is at the centre of the simulation box. 
     """
     
     type = 'btt'

MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -41,7 +41,8 @@ from MDANSE.MolecularDynamics.Trajectory import partition_universe
 
 class CenterOfMassesTrajectory(IJob):
     """
-    Creates a trajectory out of the center of masses motions for a selection of atoms of a given input trajectory
+    Creates a trajectory from the centre of masses for selected groups of atoms in a given input trajectory.
+	For a molecular system, the centre of mass trajectory will contain only the molecular translations, which are therefore separated from the rotations.
     """
     
     type = 'comt'

MDANSE/Framework/Jobs/Converters/CHARMM.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/Castep.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/Converter.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/DCDConverter.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/DL_POLY.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/Discover.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/Forcite.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/LAMMPS.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/MaterialsStudio.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/NAMD.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/PDB.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/VASP.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/Converters/XPLOR.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr

MDANSE/Framework/Jobs/CoordinationNumber.py

@@ -39,10 +39,8 @@ from MDANSE.Framework.Jobs.DistanceHistogram import DistanceHistogram
 
 class CoordinationNumber(DistanceHistogram):
     """
-    The Coordination Number computes the pair distribution function for a set of atoms, 
-    it could be defined has the total number of neighbours of a central atom in a molecule or ion. 
-    In MDANSE the definition of the Coordination Number can be seen as an extension of this previous definition, 
-    indeed, we are not only defining central atom but also centers of gravity of a set of group of atoms as center.
+    The Coordination Number is computed from the pair distribution function for a set of atoms. 
+    It describes the total number of neighbours, as a function of distance, from a central atom, or the centre of a group of atoms.
     """
 
     type = 'cn'

MDANSE/Framework/Jobs/CroppedTrajectory.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -40,7 +40,7 @@ from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 
 class CroppedTrajectory(IJob):
     """
-    Crop a trajectory as well in term of universe contents as in trajectory length..
+    Crop a trajectory in terms of the contents of the simulation box (selected atoms or molecules) and the trajectory length.
     """
     
     type = 'ct'

MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -3,8 +3,8 @@
 #Copyright (C)
 #2015- Eric C. Pellegrini Institut Laue-Langevin
 #BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
+#71 avenue des Martyrs
+#38000 Grenoble Cedex 9
 #France
 #pellegrini[at]ill.fr
 #goret[at]ill.fr
@@ -43,10 +43,10 @@ from MDANSE.Mathematics.Signal import correlation, normalize, get_spectrum
 class CurrentCorrelationFunction(IJob):
     """
     Computes the current correlation function for a set of atoms.
-    the transversal and longitudinal current correlation function are typically use to study propagation of excitations in disordered system.
-    longitudinal current are directly coupled to density fluctuation and transversal current are link to propagating 'shear modes'.
+    The transverse and longitudinal current correlation functions are typically used to study the propagation of excitations in disordered systems.
+    The longitudinal current is directly related to density fluctuations and the transverse current is linked to propagating 'shear modes'.
     
-    For more information, read 'J.-P. Hansen and I. R. McDonald, Theory of Simple Liquids (3rd ed., Elsevier), chapter 7.4: Correlations
+    For more information, see e.g. 'J.-P. Hansen and I. R. McDonald, Theory of Simple Liquids (3rd ed., Elsevier), chapter 7.4: Correlations
     in space and time)' 
     """