class Diameter(object):
r'''Container for site diameters and sigmas
**Mathematical Definition**
.. math::
\sigma_{\alpha,\beta} = (d_{\alpha} + d_{\beta})/2.0
**Variable Definitions**
:math:`d_{\alpha}`
diameter of site-type :math:`\alpha`
:math:`sigma_{\alpha,\beta}`
contact distanct between site-type :math:`\alpha` and :math:`\beta`
**Description**
A simple container class for defining the site-type diameters.
Example
-------
.. code-block:: python
import pyPRISM
d = pyPRISM.Diameter(['A','B','C'])
d['A'] = 1.0
d['B'] = 1.5
d['C'] = 5.0
d.diameter['A'] #site diameter diam_A = 1.0
d.sigma['A','B'] #site contact distance sig_AB = 1.25
d.sigma['A','C'] #site contact distance sig_AB = 3.0
'''
def __init__(self,types):
r'''Constructor
Arguments
---------
types: list
List of types of sites
Attributes
----------
diameter: :class:`pyPRISM.core.ValueTable`
Table of site site diameter values
volume: :class:`pyPRISM.core.ValueTable`
Table of site site volumes values
sigma: :class:`pyPRISM.core.PairTable`
Site-site contact distance
'''
self.types = types
self.diameter = ValueTable(types=types,name='diameter')
self.volume = ValueTable(types=types,name='volume')
self.sigma = PairTable(types=types,name='sigma')
def check(self):
'''Are all diameter set?
Raises
------
*ValueError* if diameters are not all set.
'''
self.diameter.check()
def __repr__(self):
return '<Diameter>'
def __getitem__(self,key):
key = self.diameter.listify(key)
if len(key) == 1:
return self.diameter[key[0]]
elif len(key) == 2:
return self.sigma[key[0],key[1]]
else:
ValueError('Too many types passed to diameter!')
def __setitem__(self,types1,value):
for t1 in self.diameter.listify(types1):
d1 = value
self.diameter[t1] = d1
self.volume[t1] = (4.0/3.0) * np.pi * (d1/2.0)**(3.0)
self.total = 0.
for t2 in self.types:
# If d2 isn't set yet, we can't set sigma
d2 = self.diameter[t2]
if d2 is None:
continue
self.sigma[t1,t2] = (d1 + d2)/2.0
class Density(object):
r'''Container for pair and site densities
**Mathematical Definition**
.. math::
\rho^{pair}_{\alpha,\beta} = \rho_{\alpha} \rho_{\beta}
.. math::
\rho^{site}_{\alpha,\beta} =
\begin{cases}
\rho_{\alpha} & \text{if } i = j \\
\rho_{\alpha} + \rho_{\beta} & \text{if } i \neq j
\end{cases}
.. math::
\rho^{total} = \sum_{\alpha} \rho^{site}_{\alpha,\alpha}
**Variable Definitions**
:math:`\rho_{\alpha}`
Number density of site :math:`\alpha`
:math:`\rho^{pair}_{\alpha,\beta}`
Pair number density of pair :math:`\alpha,\beta`
:math:`\rho^{site}_{\alpha,\beta}`
Site number density of pair :math:`\alpha,\beta`
:math:`\rho^{total}`
Total site number density
**Description**
This class describes the makeup of the system in terms of both total
site and pair densities. The container provides a simple interface for
getting and setting (via square brackets [ ]) site densities and also
takes care of calculating the total site and total pair number
densities. The total site and pair number densities can be accessed as
MatrixArrays (:class:`pyPRISM.core.MatrixArray`) attributes.
Example
-------
.. code-block:: python
import pyPRISM
rho = pyPRISM.Density(['A','B','C'])
rho['A'] = 0.25
rho['B'] = 0.35
rho['C'] = 0.15
rho.pair['A','B'] #pair density rho_AB = 0.25 * 0.35
rho.site['A','B'] #site density rho_AB = 0.25 + 0.35
rho.site['B','B'] #site density rho_BB = 0.35
rho.total #total density rho = 0.25 + 0.35 + 0.15
'''
def __init__(self, types):
r'''Constructor
Arguments
---------
types: list
List of types of sites
Attributes
----------
density: :class:`pyPRISM.core.ValueTable`
Table of site number density values
total: float
Total number density
site: :class:`pyPRISM.core.MatrixArray`
Site density for each pair.
pair: :class:`pyPRISM.core.MatrixArray`
Pair site density for each pair.
'''
self.types = types
self.density = ValueTable(types=types, name='density')
self.total = 0.
self.pair = MatrixArray(length=1,
rank=len(types),
types=types,
space=Space.NonSpatial)
self.site = MatrixArray(length=1,
rank=len(types),
types=types,
space=Space.NonSpatial)
def check(self):
'''Are all densities set?
Raises
------
*ValueError* if densities are not all set.
'''
self.density.check()
def __repr__(self):
return '<Density total:{:3.2f}>'.format(self.total)
def __getitem__(self, key):
return self.density[key]
def __setitem__(self, types1, value):
for t1 in self.density.listify(types1):
rho1 = value
self.density[t1] = rho1
self.total = 0.
for t2 in self.types:
# If rho2 isn't set yet, we can't set the
# site or pair densities
rho2 = self.density[t2]
if rho2 is None:
continue
self.total += rho2
# The values must be set as lists in order for them to
# be compatible with the MatrixArray type
self.pair[t1, t2] = [rho1 * rho2]
if t1 == t2:
self.site[t1, t2] = [rho1]
else:
self.site[t1, t2] = [rho1 + rho2]