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Redefined functions relating to collective diffusion coefficient and reduced ionic condictivity. #3

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Redefined functions relating to collective diffusion coefficient and reduced ionic condictivity. #3

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cf8e7a8
Redefined the necessary functions
kitmccoll Jun 25, 2020
37ff69f
Fixed error in docstrings for collective_diffusion_coefficient
kitmccoll Jul 8, 2020
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18 changes: 6 additions & 12 deletions examples/lattice_mc_examples.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,7 @@
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"import lattice_mc\n",
Expand All @@ -45,9 +43,7 @@
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"# Global variables controlling simulation parallelisation and convergence.\n",
Expand All @@ -64,9 +60,7 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"# define temperature scale\n",
Expand Down Expand Up @@ -131,7 +125,7 @@
"| correlation factor | $f$ | `Simulation.tracer_correlation` | \n",
"| collective correlation factor | $f_\\mathrm{I}$ | `Simulation.collective_correlation` |\n",
"| tracer diffusion coefficient | $D^*$ | `Simulation.tracer_diffusion_coefficient` |\n",
"| “jump” diffusion coefficient | $D_\\mathrm{J}$ | `Simulation.collective_diffusion_coefficient` |\n",
"| “jump” diffusion coefficient | $D_\\mathrm{J}$ | `Simulation.collective_diffusion_coefficient_per_atom` |\n",
"| average site occupations | occ($\\alpha$) | `Simulation.average_site_occupations` |"
]
},
Expand All @@ -157,7 +151,7 @@
"print( \"f = {}\".format( s.tracer_correlation ) )\n",
"print( \"f_I = {}\".format( s.collective_correlation ) )\n",
"print( \"D* = {:.3e}\".format( s.tracer_diffusion_coefficient ) )\n",
"print( \"D_J = {:.3e}\".format( s.collective_diffusion_coefficient ) )\n",
"print( \"D_J = {:.3e}\".format( s.collective_diffusion_coefficient_per_atom ) )\n",
"# Simulation.average_site_occupations returns a dictionary\n",
"for k, v in s.average_site_occupations.items():\n",
" print( \"occ({}) = {:f}\".format( k, v ) )"
Expand All @@ -184,7 +178,7 @@
"source": [
"def simulation_wrapper(_):\n",
" s = run_simulation()\n",
" return s.tracer_correlation, s.collective_correlation, s.tracer_diffusion_coefficient, s.collective_diffusion_coefficient"
" return s.tracer_correlation, s.collective_correlation, s.tracer_diffusion_coefficient, s.collective_diffusion_coefficient_per_atom"
]
},
{
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30 changes: 25 additions & 5 deletions lattice_mc/simulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -271,23 +271,25 @@ def collective_correlation( self ):
return None

@property
def reduced_ionic_conductivity( self ):
def collective_diffusion_coefficient( self ):
"""
Returns the reduced ionic conductivity, \u03C3\' ( D_J * n_natoms).
Returns the collective or "jump" diffusion coefficient multiplied by the number of atoms,
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@bjmorgan bjmorgan Jul 8, 2020

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This is potentially misleading. This method returns the collective diffusion coefficient, which is equal to the "jump" diffusion coefficient multiplied by the number of atoms, D_J * N.

( D_J * number_of_atoms).

Args:
None

Returns:
(Float): The reduced ionic conductivity, \u03C3\' ( D_J * n_natoms).
(Float): the collective or "jump" diffusion coefficient multiplied by the number of
atoms, ( D_J * number_of_atoms).
Comment on lines +283 to +284
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@bjmorgan bjmorgan Jul 8, 2020

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Also needs changing here.

"""
if self.has_run:
return self.atoms.collective_dr_squared() / ( 6.0 * self.lattice.time )
else:
return None

@property
def collective_diffusion_coefficient( self ):
def collective_diffusion_coefficient_per_atom( self ):
"""
Returns the collective or "jump" diffusion coefficient, D_J.
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@bjmorgan bjmorgan Jul 8, 2020

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This is incorrect. Returns the collective diffusion coefficient per atom, which is equal to the "jump" diffusion coefficient.


Expand All @@ -298,7 +300,25 @@ def collective_diffusion_coefficient( self ):
(Float): The collective diffusion coefficient, D_J.
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@bjmorgan bjmorgan Jul 8, 2020

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Inconsistent. The collective diffusion coefficient is D_J * N_atoms.

"""
if self.has_run:
return self.reduced_ionic_conductivity / float( self.number_of_atoms )
return self.collective_diffusion_coefficient / float( self.number_of_atoms )
else:
return None

@property
def reduced_ionic_conductivity( self ):
"""
Returns the reduced ionic conductivity, \u03C3\' ( D_J * ( number_of_atoms /
number_of_sites ) ).

Args:
None

Returns:
(Float): The reduced ionic conductivity, \u03C3\' ( D_J * ( number_of_atoms /
number_of_sites )).
"""
if self.has_run:
return self.atoms.collective_diffusion_coefficient_per_atom * float( self.number_of_atoms / self.number_of_sites )
else:
return None

Expand Down