Commit e5a3448a authored by Mark Robert Johnson's avatar Mark Robert Johnson
Browse files

Change of address in all files in Jobs directory and sub-directory.

Update of help text for all analyses.
parent 925b4b4b
......@@ -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
......
......@@ -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'
......
......@@ -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'
......
......@@ -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'
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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'
......
......@@ -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'
......
......@@ -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)'
"""
......
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