[cig-commits] [commit] master: molar_fraction to molar_fractions (for consistency) (2990e1f)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Fri Dec 12 21:32:57 PST 2014
Repository : https://github.com/geodynamics/burnman
On branch : master
Link : https://github.com/geodynamics/burnman/compare/881b878da7bd7228b4e714d9d10c4a75c876efb6...7c010ac6610ee014aabcb76a2a4f667a06a8e7f7
>---------------------------------------------------------------
commit 2990e1f46d8781580a322de25c19638cf4c89a13
Author: Bob Myhill <myhill.bob at gmail.com>
Date: Fri Dec 12 21:00:48 2014 -0800
molar_fraction to molar_fractions (for consistency)
>---------------------------------------------------------------
2990e1f46d8781580a322de25c19638cf4c89a13
burnman/solidsolution.py | 8 +--
burnman/solutionmodel.py | 89 ++++++++++++++---------------
misc/benchmarks/solidsolution_benchmarks.py | 17 +++---
3 files changed, 55 insertions(+), 59 deletions(-)
diff --git a/burnman/solidsolution.py b/burnman/solidsolution.py
index 7dcc85e..cee8daf 100644
--- a/burnman/solidsolution.py
+++ b/burnman/solidsolution.py
@@ -98,8 +98,8 @@ class SolidSolution(Mineral):
self.K_S = self.K_T*self.C_p/self.C_v
self.gr = self.alpha*self.K_T*self.V/self.C_v
- def calcgibbs(self, pressure, temperature, molar_fractions):
- return sum([ self.base_material[i][0].calcgibbs(pressure, temperature) * molar_fractions[i] for i in range(self.n_endmembers) ]) + self.solution_model.excess_gibbs_free_energy( pressure, temperature, molar_fractions)
+ def calcgibbs(self, pressure, temperature, molar_fraction):
+ return sum([ self.base_material[i][0].calcgibbs(pressure, temperature) * molar_fraction[i] for i in range(self.n_endmembers) ]) + self.solution_model.excess_gibbs_free_energy( pressure, temperature, molar_fraction)
- def calcpartialgibbsexcesses(self, pressure, temperature, molar_fractions):
- return self.solution_model.excess_partial_gibbs_free_energies(self, pressure, temperature, molar_fractions)
+ def calcpartialgibbsexcesses(self, pressure, temperature, molar_fraction):
+ return self.solution_model.excess_partial_gibbs_free_energies(self, pressure, temperature, molar_fraction)
diff --git a/burnman/solutionmodel.py b/burnman/solutionmodel.py
index e12dba3..30d4d5f 100644
--- a/burnman/solutionmodel.py
+++ b/burnman/solutionmodel.py
@@ -33,7 +33,7 @@ class SolutionModel(object):
"""
pass
- def excess_gibbs_free_energy( self, pressure, temperature, molar_fractions):
+ def excess_gibbs_free_energy( self, pressure, temperature, molar_fraction):
"""
Given a list of molar fractions of different phases,
compute the excess Gibbs free energy of the solution.
@@ -48,7 +48,7 @@ class SolutionModel(object):
temperature : float
Temperature at which to evaluate the solution. [K]
- molar_fractions : list of floats
+ molar_fraction : list of floats
List of molar fractions of the different endmembers in solution
Returns
@@ -56,9 +56,9 @@ class SolutionModel(object):
G_excess : float
The excess Gibbs free energy
"""
- return np.dot(np.array(molar_fractions), self.excess_partial_gibbs_free_energies( pressure, temperature, molar_fractions))
+ return np.dot(np.array(molar_fraction), self.excess_partial_gibbs_free_energies( pressure, temperature, molar_fraction))
- def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fractions):
+ def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fraction):
"""
Given a list of molar fractions of different phases,
compute the excess Gibbs free energy for each endmember of the solution.
@@ -73,7 +73,7 @@ class SolutionModel(object):
temperature : float
Temperature at which to evaluate the solution. [K]
- molar_fractions : list of floats
+ molar_fraction : list of floats
List of molar fractions of the different endmembers in solution
Returns
@@ -81,9 +81,9 @@ class SolutionModel(object):
partial_G_excess : numpy array
The excess Gibbs free energy of each endmember
"""
- return np.empty_like( np.array(molar_fractions) )
+ return np.empty_like( np.array(molar_fraction) )
- def excess_volume( self, pressure, temperature, molar_fractions):
+ def excess_volume( self, pressure, temperature, molar_fraction):
"""
Given a list of molar fractions of different phases,
compute the excess Gibbs free energy of the solution,
@@ -97,7 +97,7 @@ class SolutionModel(object):
temperature : float
Temperature at which to evaluate the solution. [K]
- molar_fractions : list of floats
+ molar_fraction : list of floats
List of molar fractions of the different endmembers in solution
Returns
@@ -115,7 +115,6 @@ class IdealSolution (SolutionModel):
entropy, all the other excess terms return zero.
"""
def __init__(self, endmembers):
-
self.n_endmembers = len(endmembers)
self.formulas = [e[1] for e in endmembers]
@@ -125,8 +124,8 @@ class IdealSolution (SolutionModel):
self._calculate_endmember_configurational_entropies()
- def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fractions ):
- return self._ideal_excess_partial_gibbs( temperature, molar_fractions )
+ def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fraction ):
+ return self._ideal_excess_partial_gibbs( temperature, molar_fraction )
def _calculate_endmember_configurational_entropies( self ):
self.endmember_configurational_entropies=np.zeros(shape=(self.n_endmembers))
@@ -137,11 +136,11 @@ class IdealSolution (SolutionModel):
self.endmember_configurational_entropies[idx] - \
constants.gas_constant*self.site_multiplicities[occ]*endmember_occupancy[occ]*np.log(endmember_occupancy[occ])
- def _endmember_configurational_entropy_contribution(self, molar_fractions):
- return np.dot(molar_fractions, self.endmember_configurational_entropies)
+ def _endmember_configurational_entropy_contribution(self, molar_fraction):
+ return np.dot(molar_fraction, self.endmember_configurational_entropies)
- def _configurational_entropy (self, molar_fractions):
- site_occupancies=np.dot(molar_fractions, self.endmember_occupancies)
+ def _configurational_entropy (self, molar_fraction):
+ site_occupancies=np.dot(molar_fraction, self.endmember_occupancies)
conf_entropy=0
for idx, occupancy in enumerate(site_occupancies):
if occupancy > 1e-10:
@@ -150,11 +149,11 @@ class IdealSolution (SolutionModel):
return conf_entropy
- def _ideal_excess_partial_gibbs( self, temperature, molar_fractions ):
- return constants.gas_constant*temperature * self._log_ideal_activities(molar_fractions)
+ def _ideal_excess_partial_gibbs( self, temperature, molar_fraction ):
+ return constants.gas_constant*temperature * self._log_ideal_activities(molar_fraction)
- def _log_ideal_activities ( self, molar_fractions ):
- site_occupancies=np.dot(molar_fractions, self.endmember_occupancies)
+ def _log_ideal_activities ( self, molar_fraction ):
+ site_occupancies=np.dot(molar_fraction, self.endmember_occupancies)
lna=np.empty(shape=(self.n_endmembers))
for e in range(self.n_endmembers):
@@ -167,8 +166,8 @@ class IdealSolution (SolutionModel):
lna[e]=lna[e] + self.endmember_configurational_entropies[e]/constants.gas_constant
return lna
- def _ideal_activities ( self, molar_fractions ):
- site_occupancies=np.dot(molar_fractions, self.endmember_occupancies)
+ def _ideal_activities ( self, molar_fraction ):
+ site_occupancies=np.dot(molar_fraction, self.endmember_occupancies)
activities=np.empty(shape=(self.n_endmembers))
for e in range(self.n_endmembers):
@@ -216,21 +215,21 @@ class AsymmetricRegularSolution (IdealSolution):
#initialize ideal solution model
IdealSolution.__init__(self, endmembers )
- def _phi( self, molar_fractions):
- phi=np.array([self.alpha[i]*molar_fractions[i] for i in range(self.n_endmembers)])
+ def _phi( self, molar_fraction):
+ phi=np.array([self.alpha[i]*molar_fraction[i] for i in range(self.n_endmembers)])
phi=np.divide(phi, np.sum(phi))
return phi
- def _non_ideal_interactions( self, molar_fractions ):
+ def _non_ideal_interactions( self, molar_fraction ):
# -sum(sum(qi.qj.Wij*)
# equation (2) of Holland and Powell 2003
- phi=self._phi(molar_fractions)
+ phi=self._phi(molar_fraction)
- q=np.zeros(len(molar_fractions))
- Hint=np.zeros(len(molar_fractions))
- Sint=np.zeros(len(molar_fractions))
- Vint=np.zeros(len(molar_fractions))
+ q=np.zeros(len(molar_fraction))
+ Hint=np.zeros(len(molar_fraction))
+ Sint=np.zeros(len(molar_fraction))
+ Vint=np.zeros(len(molar_fraction))
for l in range(self.n_endmembers):
q=np.array([kd(i,l)-phi[i] for i in range(self.n_endmembers)])
@@ -241,32 +240,32 @@ class AsymmetricRegularSolution (IdealSolution):
return Hint, Sint, Vint
- def _non_ideal_excess_partial_gibbs( self, pressure, temperature, molar_fractions) :
+ def _non_ideal_excess_partial_gibbs( self, pressure, temperature, molar_fraction) :
- Hint, Sint, Vint = self._non_ideal_interactions( molar_fractions )
+ Hint, Sint, Vint = self._non_ideal_interactions( molar_fraction )
return Hint - temperature*Sint + pressure*Vint
- def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fractions ):
+ def excess_partial_gibbs_free_energies( self, pressure, temperature, molar_fraction ):
- ideal_gibbs = IdealSolution._ideal_excess_partial_gibbs (self, temperature, molar_fractions )
- non_ideal_gibbs = self._non_ideal_excess_partial_gibbs(pressure, temperature, molar_fractions)
+ ideal_gibbs = IdealSolution._ideal_excess_partial_gibbs (self, temperature, molar_fraction )
+ non_ideal_gibbs = self._non_ideal_excess_partial_gibbs(pressure, temperature, molar_fraction)
return ideal_gibbs + non_ideal_gibbs
- def excess_volume ( self, pressure, temperature, molar_fractions ):
- phi=self._phi(molar_fractions)
- V_excess=np.dot(self.alpha.T,molar_fractions)*np.dot(phi.T,np.dot(self.Wv,phi))
+ def excess_volume ( self, pressure, temperature, molar_fraction ):
+ phi=self._phi(molar_fraction)
+ V_excess=np.dot(self.alpha.T,molar_fraction)*np.dot(phi.T,np.dot(self.Wv,phi))
return V_excess
- def excess_entropy( self, pressure, temperature, molar_fractions ):
- phi=self._phi(molar_fractions)
- S_conf=np.dot(IdealSolution._ideal_excess_partial_gibbs(self, temperature, molar_fractions),molar_fractions)
- S_excess=np.dot(self.alpha.T,molar_fractions)*np.dot(phi.T,np.dot(self.Ws,phi))
+ def excess_entropy( self, pressure, temperature, molar_fraction ):
+ phi=self._phi(molar_fraction)
+ S_conf=np.dot(IdealSolution._ideal_excess_partial_gibbs(self, temperature, molar_fraction),molar_fraction)
+ S_excess=np.dot(self.alpha.T,molar_fraction)*np.dot(phi.T,np.dot(self.Ws,phi))
return S_conf + S_excess
- def excess_enthalpy( self, pressure, temperature, molar_fractions ):
- phi=self._phi(molar_fractions)
- H_excess=np.dot(self.alpha.T,molar_fractions)*np.dot(phi.T,np.dot(self.Wh,phi))
- return H_excess + pressure*self.excess_volume ( pressure, temperature, molar_fractions )
+ def excess_enthalpy( self, pressure, temperature, molar_fraction ):
+ phi=self._phi(molar_fraction)
+ H_excess=np.dot(self.alpha.T,molar_fraction)*np.dot(phi.T,np.dot(self.Wh,phi))
+ return H_excess + pressure*self.excess_volume ( pressure, temperature, molar_fraction )
class SymmetricRegularSolution (AsymmetricRegularSolution):
diff --git a/misc/benchmarks/solidsolution_benchmarks.py b/misc/benchmarks/solidsolution_benchmarks.py
index 21c2986..65ec5b9 100644
--- a/misc/benchmarks/solidsolution_benchmarks.py
+++ b/misc/benchmarks/solidsolution_benchmarks.py
@@ -13,8 +13,6 @@ import matplotlib.image as mpimg
atomic_masses=read_masses()
-
-
'''
Solvus shapes (a proxy for Gibbs free energy checking
'''
@@ -54,10 +52,10 @@ sp=o_d_spinel()
sp_entropies = np.empty_like(comp)
sp_entropies_NK1967= np.empty_like(comp)
for i,c in enumerate(comp):
- molar_fractions=[1.0-c, c]
- sp.set_composition( np.array(molar_fractions) )
+ molar_fraction=[1.0-c, c]
+ sp.set_composition( np.array(molar_fraction) )
sp.set_state( 1e5, 298.15 )
- sp_entropies[i] = sp.solution_model._configurational_entropy( molar_fractions )
+ sp_entropies[i] = sp.solution_model._configurational_entropy( molar_fraction )
sp_entropies_NK1967[i] = -8.3145*(c*np.log(c) + (1.-c)*np.log(1.-c) + c*np.log(c/2.) + (2.-c)*np.log(1.-c/2.)) # eq. 7 in Navrotsky and Kleppa, 1967.
#fig1 = mpimg.imread('configurational_entropy.png') # Uncomment these two lines if you want to overlay the plot on a screengrab from SLB2011
@@ -134,11 +132,10 @@ opx_models=[orthopyroxene_red(), orthopyroxene_blue(), orthopyroxene_long_dashed
opx_entropies = [ np.empty_like(comp) for model in opx_models ]
for idx, model in enumerate(opx_models):
for i,c in enumerate(comp):
- molar_fractions=[1.0-c, c]
- model.set_composition( np.array(molar_fractions) )
- model.set_state( 0., 0. )
- opx_entropies[idx][i] = model.solution_model._configurational_entropy( molar_fractions )
-
+ molar_fraction=[1.0-c, c]
+ model.set_composition(np.array(molar_fraction))
+ model.set_state(0., 0.)
+ opx_entropies[idx][i] = model.solution_model._configurational_entropy(molar_fraction)
fig1 = mpimg.imread('configurational_entropy.png') # Uncomment these two lines if you want to overlay the plot on a screengrab from SLB2011
plt.imshow(fig1, extent=[0.0, 1.0,0.,17.0], aspect='auto')
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