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Scientific Software
MDANSE
Commits
7bd2071e
Commit
7bd2071e
authored
Jun 09, 2015
by
eric pellegrini
Browse files
Merge branch 'master' of git@github.com:eurydyce/MDANSE.git
parents
346bfbe1
abe59b48
Changes
51
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MDANSE/Framework/Jobs/AngularCorrelation.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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 cent
e
r definition
. In this particular case
the origin
is the head group geometric center designated with the spher
e and the direction
is
simply the last atom
of the tail chain. The correlation is calculated for the angle formed b
etween
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 centr
e
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 molecul
e and the direction simply
by
the last atom
of the tail
or
chain. The correlation is calculated for the angle formed b
y
the same vector at
different times
**Calculation:**
\n
...
...
MDANSE/Framework/Jobs/AreaPerMolecule.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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
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7bd2071e
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@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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 cent
e
r 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 centr
e
of the simulation box.
"""
type
=
'btt'
...
...
MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/Castep.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/Converter.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/DCDConverter.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/DL_POLY.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/Discover.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/Forcite.py
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7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/LAMMPS.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/MaterialsStudio.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/NAMD.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/PDB.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/VASP.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/Converters/XPLOR.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
Grenoble Cedex 9
#France
#pellegrini[at]ill.fr
#goret[at]ill.fr
...
...
MDANSE/Framework/Jobs/CoordinationNumber.py
View file @
7bd2071e
...
...
@@ -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
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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 term
s
of
the contents of the simulation box (selected atoms or molecules) and the
trajectory length.
"""
type
=
'ct'
...
...
MDANSE/Framework/Jobs/CurrentCorrelationFunction.py
View file @
7bd2071e
...
...
@@ -3,8 +3,8 @@
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin
#BP 156
#
6, rue Jules Horowitz
#380
42
Grenoble Cedex 9
#
71 avenue des Martyrs
#380
00
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.
t
he transvers
al
and longitudinal current correlation function are typically use to study propagation of excitations in disordered system.
longitudinal current
are
directly
coupl
ed to density fluctuation and transvers
al
current
are
link to propagating 'shear modes'.
T
he transvers
e
and longitudinal current correlation function
s
are typically use
d
to study
the
propagation of excitations in disordered system
s
.
The
longitudinal current
is
directly
relat
ed to density fluctuation
s
and
the
transvers
e
current
is
link
ed
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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