Commit cdf974c1 authored by eric pellegrini's avatar eric pellegrini

Improved docuentation for VACF

Bug fix in conf.py sphinx configuration file
parent 9f2e95dd
......@@ -147,9 +147,13 @@ def flag_onthefly(app, what, name, obj, options, lines):
if what in members_to_watch:
# modify the docstring so the rendered output is highlights the omission
if lines:
lines.insert(0,'\n:Description:\n\n')
# lines.insert(0,' .. inheritance-diagram:: %s' % name.split('.')[-1])
# lines.insert(0,'**inheritance-diagram:**')
lines.insert(0,'')
lines.insert(0,':Description:')
lines.insert(0,'')
lines.insert(0,'.. inheritance-diagram:: %s' % name.split('.')[-1])
lines.insert(0,'')
lines.insert(0,'**Inheritance-diagram:**')
lines.insert(0,'')
def setup(app):
......
......@@ -54,11 +54,11 @@ class MeanSquareDisplacement(IJob):
.. math:: <r^{2}> = 6Dt + C
where <r^2> is the MSD and t is the time. D and C are constants. The constant D is
where :math:`<r^{2}>` is the MSD and t is the time. D and C are constants. The constant D is
the so-called diffusion coefficient.
More generally the MSD reveals the distance or volume explored by atoms and molecules as a function of time.
In crystals the MSD quickly saturates at a constant value which corresponds to the vibrational amplitude.
In crystals, the MSD quickly saturates at a constant value which corresponds to the vibrational amplitude.
Diffusion in a volume will also have a limiting value of the MSD which corresponds to the diameter of the volume
and the saturation value is reached more slowly.
The MSD can also reveal e.g. sub-diffusion regimes for the translational diffusion of lipids in membranes.
......
......@@ -53,8 +53,17 @@ class VelocityAutoCorrelationFunction(IJob):
In the liquid phase, the atoms have more freedom than in the solid phase and because of the diffusion process, the oscillatory motion
seen in solid phase is damped rapidly depending on the density of the system. So, the VACF tends to have one very damped oscillation
before decaying to zero. The decaying time can be considered as the average time for a collision between two atoms. The integral of
the VACF is proportional to the diffusion constant (D/3).
before decaying to zero. The decaying time can be considered as the average time for a collision between two atoms.
As well as revealing the dynamical processes in a system, the VACF has other interesting properties. Firstly, its Fourier transform,
a.k.a as vibrational Density Of States (vDOS) can be used to reveal the underlying frequencies of the molecular processes. This is closely
related to the infra-red spectrum of the system, which is also concerned with vibration on the molecular scale. Secondly, provided the VACF
decays to zero at long time, the function may be integrated mathematically to calculate the diffusion coefficient D, as in:
.. math:: D = \\frac{1}{3}\int_{0}^{+\infty}{<v(0) \cdot v(t)>dt}
This is a special case of a more general relationship between the VACF and the mean square displacement, and belongs to a class of properties
known as the Green-Kubo relations, which relate correlation functions to so-called transport coefficients.
"""
type = 'vacf'
......
......@@ -175,14 +175,14 @@ class BuildDoc(_BuildDoc):
# Run sphinx by calling the main method, '--full' also adds a conf.py
sphinx.apidoc.main(['', '-F','--separate', '-H', metadata.name, '-A', metadata.author,
'-V', metadata.version, '-R', metadata.version,
'-o', 'fuck', os.path.join(os.path.abspath(build.build_lib),'MDANSE'),os.path.join(os.path.abspath(build.build_lib),'MDANSE','Externals')])
'-o', 'sphinx_temp_rst', os.path.join(os.path.abspath(build.build_lib),'MDANSE'),os.path.join(os.path.abspath(build.build_lib),'MDANSE','Externals')])
import shutil
shutil.copy(os.path.join('Doc','conf.py'),'fuck')
shutil.copy(os.path.join('Doc','mdanse_logo.png'),os.path.join('fuck','_static'))
shutil.copy(os.path.join('Doc','layout.html'),os.path.join('fuck','_templates'))
shutil.copy(os.path.join('Doc','conf.py'),'sphinx_temp_rst')
shutil.copy(os.path.join('Doc','mdanse_logo.png'),os.path.join('sphinx_temp_rst','_static'))
shutil.copy(os.path.join('Doc','layout.html'),os.path.join('sphinx_temp_rst','_templates'))
self.source_dir = 'fuck'
self.source_dir = 'sphinx_temp_rst'
self.config_dir = self.source_dir
self.build_dir = os.path.join(os.path.abspath(build.build_lib),'MDANSE','Doc')
......
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