[cig-commits] [commit] master: move EOS into sub-package, rework imports, cleanup, documentation (4d4cd9f)

[cig_noreply at geodynamics.org]

Repository : https://github.com/geodynamics/burnman

On branch  : master
Link       : https://github.com/geodynamics/burnman/compare/53964ef9adcc1f8b89f9e48ae774c2ecb51f216a...6f75d3766c3c8e3bf6599b894e7bbe2993f57419

>---------------------------------------------------------------

commit 4d4cd9fb374acee329be079afa04a2676a271302
Author: Timo Heister <timo.heister at gmail.com>
Date:   Fri Dec 12 13:24:23 2014 -0800

    move EOS into sub-package, rework imports, cleanup, documentation


>---------------------------------------------------------------

4d4cd9fb374acee329be079afa04a2676a271302
 burnman/__init__.py                       | 14 +++++----
 burnman/composite.py                      |  5 ++--
 burnman/{ => eos}/birch_murnaghan.py      |  4 ++-
 burnman/{ => eos}/cork.py                 |  4 +--
 burnman/{ => eos}/einstein.py             |  3 +-
 burnman/{ => eos}/equation_of_state.py    |  2 +-
 burnman/{ => eos}/mie_grueneisen_debye.py |  2 +-
 burnman/{ => eos}/modified_tait.py        |  7 ++---
 burnman/{ => eos}/slb.py                  |  2 +-
 burnman/geotherm.py                       |  2 +-
 burnman/main.py                           |  1 +
 burnman/mineral.py                        | 47 +++++--------------------------
 burnman/mineral_helpers.py                | 15 +++++-----
 burnman/minerals/__init__.py              |  1 -
 burnman/solidsolution.py                  | 41 +++++++++++++++++++--------
 burnman/solutionmodel.py                  | 23 +++++++++++----
 tests/test_eos.py                         |  4 +--
 17 files changed, 88 insertions(+), 89 deletions(-)

diff --git a/burnman/__init__.py b/burnman/__init__.py
index 5f34555..c32eba1 100644
--- a/burnman/__init__.py
+++ b/burnman/__init__.py
@@ -51,26 +51,28 @@ Acknowledgement and Support:
 
 from version import version as __version__
 
-#classes for representing rocks and minerals
+# classes for representing rocks and minerals:
 from mineral import Mineral
 from material import Material
 from composite import Composite
 from solidsolution import SolidSolution
 from mineral_helpers import *
 
-#high level functions
+# high level functions
 from main import *
 from model import Model
 
-#mineral library
+# mineral library
 import minerals
 
-#central user tools
+# central user tools
 import seismic
 import averaging_schemes
-import solutionmodel
+import eos
+
+from solutionmodel import SolutionModel
 import geotherm
 
-#miscellaneous
+# miscellaneous
 import tools
 from partitioning import calculate_partition_coefficient,calculate_phase_percents
diff --git a/burnman/composite.py b/burnman/composite.py
index c7521d8..da933d8 100644
--- a/burnman/composite.py
+++ b/burnman/composite.py
@@ -5,9 +5,8 @@
 import numpy as np
 import warnings
 
-from burnman.material import Material
-from burnman.mineral import Mineral
-
+from burnman import Material
+from burnman import Mineral
 
 def check_pairs(fractions, minerals):
         if len(fractions) < 1:
diff --git a/burnman/birch_murnaghan.py b/burnman/eos/birch_murnaghan.py
similarity index 99%
rename from burnman/birch_murnaghan.py
rename to burnman/eos/birch_murnaghan.py
index d0fc4f0..40a1dcc 100644
--- a/burnman/birch_murnaghan.py
+++ b/burnman/eos/birch_murnaghan.py
@@ -3,7 +3,8 @@
 # Released under GPL v2 or later.
 
 import scipy.optimize as opt
-import burnman.equation_of_state as eos
+import equation_of_state as eos
+
 
 def bulk_modulus(volume, params):
     """
@@ -20,6 +21,7 @@ def bulk_modulus(volume, params):
            5*params['K_0'] ) * f + 27./2. * (params['K_0']*params['Kprime_0'] - 4.* params['K_0'])*f*f)
     return K
 
+
 def birch_murnaghan(x, params):
     """
     equation for the third order birch-murnaghan equation of state, returns
diff --git a/burnman/cork.py b/burnman/eos/cork.py
similarity index 98%
rename from burnman/cork.py
rename to burnman/eos/cork.py
index f98e2ba..ce4e09c 100644
--- a/burnman/cork.py
+++ b/burnman/eos/cork.py
@@ -8,8 +8,8 @@
 import numpy as np
 import scipy.optimize as opt
 
-import burnman.equation_of_state as eos
-import constants
+import equation_of_state as eos
+import burnman.constants as constants
 
 T_0=298.15 # Standard temperature = 25 C
 P_0=1.e5 # Standard pressure = 1.e5 Pa
diff --git a/burnman/einstein.py b/burnman/eos/einstein.py
similarity index 97%
rename from burnman/einstein.py
rename to burnman/eos/einstein.py
index b4053f8..66fa392 100644
--- a/burnman/einstein.py
+++ b/burnman/eos/einstein.py
@@ -3,7 +3,7 @@
 # Released under GPL v2 or later.
 
 import numpy as np
-import constants
+import burnman.constants as constants
 
 """
 Functions for the Einstein model of a solid.
@@ -22,6 +22,7 @@ def thermal_energy(T, einstein_T, n):
     E_th = 3.*n*constants.gas_constant*einstein_T*( 0.5 + 1. / (np.exp( x ) - 1.0) ) # include the zero point energy
     return E_th
 
+
 def heat_capacity_v(T,einstein_T,n):
     """
     Heat capacity at constant volume.  In J/K/mol
diff --git a/burnman/equation_of_state.py b/burnman/eos/equation_of_state.py
similarity index 100%
rename from burnman/equation_of_state.py
rename to burnman/eos/equation_of_state.py
index 2fe41ae..47e7fe2 100644
--- a/burnman/equation_of_state.py
+++ b/burnman/eos/equation_of_state.py
@@ -1,8 +1,8 @@
-
 # BurnMan - a lower mantle toolkit
 # Copyright (C) 2012, 2013, Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
 # Released under GPL v2 or later.
 
+
 class EquationOfState(object):
     """
     This class defines the interface for an equation of state
diff --git a/burnman/mie_grueneisen_debye.py b/burnman/eos/mie_grueneisen_debye.py
similarity index 99%
rename from burnman/mie_grueneisen_debye.py
rename to burnman/eos/mie_grueneisen_debye.py
index b5b3603..6bc0d26 100644
--- a/burnman/mie_grueneisen_debye.py
+++ b/burnman/eos/mie_grueneisen_debye.py
@@ -8,7 +8,7 @@ import scipy.optimize as opt
 import burnman.equation_of_state as eos
 import burnman.birch_murnaghan as bm
 import burnman.debye as debye
-import constants
+import burnman.constants as constants
 
 class MGDBase(eos.EquationOfState):
     """
diff --git a/burnman/modified_tait.py b/burnman/eos/modified_tait.py
similarity index 99%
rename from burnman/modified_tait.py
rename to burnman/eos/modified_tait.py
index bb42824..5196a5d 100644
--- a/burnman/modified_tait.py
+++ b/burnman/eos/modified_tait.py
@@ -3,12 +3,11 @@
 # Released under GPL v2 or later.
 
 import numpy as np
-import scipy.optimize as opt
 
-import burnman.equation_of_state as eos
-import burnman.einstein as einstein
+import equation_of_state as eos
+import einstein
 from burnman.endmemberdisorder import *
-import constants
+import burnman.constants as constants
 
 T_0=298.15 # Standard temperature = 25 C
 P_0=1.e5 # Standard pressure = 1.e5 Pa
diff --git a/burnman/slb.py b/burnman/eos/slb.py
similarity index 99%
rename from burnman/slb.py
rename to burnman/eos/slb.py
index 11baec0..c4a50b8 100644
--- a/burnman/slb.py
+++ b/burnman/eos/slb.py
@@ -8,7 +8,7 @@ import warnings
 
 import burnman.birch_murnaghan as bm
 import burnman.debye as debye
-import burnman.equation_of_state as eos
+import equation_of_state as eos
 
 class SLBBase(eos.EquationOfState):
     """
diff --git a/burnman/geotherm.py b/burnman/geotherm.py
index 5faf0f7..9e3c418 100644
--- a/burnman/geotherm.py
+++ b/burnman/geotherm.py
@@ -3,11 +3,11 @@
 # Released under GPL v2 or later.
 
 import numpy as np
-import matplotlib.pyplot as pyplot
 import scipy.integrate as integrate
 import tools
 import seismic
 
+
 def brown_shankland(pressure):
     """
     Geotherm from Brown and Shankland (1981).
diff --git a/burnman/main.py b/burnman/main.py
index eb27e74..5801f21 100644
--- a/burnman/main.py
+++ b/burnman/main.py
@@ -9,6 +9,7 @@ import burnman.geotherm
 import burnman.seismic
 import burnman.averaging_schemes
 
+
 class ElasticProperties(object):
     """
     Class that contains volume, density, and moduli. This is generated for
diff --git a/burnman/mineral.py b/burnman/mineral.py
index 9733652..aa0bb18 100644
--- a/burnman/mineral.py
+++ b/burnman/mineral.py
@@ -7,13 +7,8 @@ import warnings
 import numpy as np
 
 from burnman.material import Material
-import burnman.equation_of_state as eos
-import burnman.birch_murnaghan as bm
-import burnman.slb as slb
-import burnman.mie_grueneisen_debye as mgd
-import inspect
-import burnman.modified_tait as mt
-import burnman.cork as cork
+import burnman.eos as eos
+
 
 class Mineral(Material):
     """
@@ -43,12 +38,12 @@ class Mineral(Material):
 
     def __init__(self):
         if 'params' not in self.__dict__:
-            self.params={}
+            self.params = {}
         self.method = None
         if 'equation_of_state' in self.params:
             self.set_method(self.params['equation_of_state'])
 
-    def set_method(self, method):
+    def set_method(self, equation_of_state):
         """
         Set the equation of state to be used for this mineral.
         Takes a string corresponding to any of the predefined
@@ -57,41 +52,13 @@ class Mineral(Material):
         class which derives from the equation_of_state base class.
         """
 
-        if method is None:
+        if equation_of_state is None:
             self.method = None
             return
 
-        def to_method_obj(method):
-
-            if isinstance(method, basestring):
-                if (method == "slb2"):
-                    return slb.SLB2()
-                elif (method == "mgd2"):
-                    return mgd.MGD2()
-                elif (method == "mgd3"):
-                    return mgd.MGD3()
-                elif (method == "slb3"):
-                    return slb.SLB3()
-                elif (method == "bm2"):
-                    return bm.BM2()
-                elif (method == "bm3"):
-                    return bm.BM3()
-                elif (method == "mtait"):
-                    return mt.MT()
-                elif (method == "cork"):
-                    return cork.CORK()
-                else:
-                    raise Exception("unsupported material method " + method)
-            elif isinstance(method, eos.EquationOfState):
-                return method
-            elif inspect.isclass(method) and issubclass(method, eos.EquationOfState):
-                return method()
-            else:
-                raise Exception("unsupported material method " + method.__class__.__name__ )
-
-        new_method = to_method_obj(method)
+        new_method = eos.create(equation_of_state)
         if self.method is not None and 'equation_of_state' in self.params:
-            self.method = to_method_obj(self.params['equation_of_state'])
+            self.method = eos.create(self.params['equation_of_state'])
 
         if type(new_method).__name__ == 'instance':
             raise Exception("Please derive your method from object (see python old style classes)")
diff --git a/burnman/mineral_helpers.py b/burnman/mineral_helpers.py
index ace9683..cd605d7 100644
--- a/burnman/mineral_helpers.py
+++ b/burnman/mineral_helpers.py
@@ -11,13 +11,12 @@ This module provides several helper minerals/materials.
 import numpy as np
 import warnings
 
-from burnman.material import Material
+from burnman import Material, Mineral
 
-from burnman.mineral import Mineral
-import burnman.equation_of_state as eos
-import burnman.birch_murnaghan as bm
-import burnman.slb as slb
-import burnman.mie_grueneisen_debye as mgd
+#import burnman.equation_of_state as eos
+#import burnman.birch_murnaghan as bm
+#import burnman.slb as slb
+#import burnman.mie_grueneisen_debye as mgd
 
 
 class HelperSolidSolution(Mineral):
@@ -52,9 +51,9 @@ class HelperSolidSolution(Mineral):
         
         self.params = {}
 
-    def set_method(self, method):
+    def set_method(self, equation_of_state):
         for m in self.base_materials:
-            m.set_method(method)
+            m.set_method(equation_of_state)
 
     def debug_print(self, indent=""):
         print "%sHelperSolidSolution(%s):" % (indent, self.to_string())
diff --git a/burnman/minerals/__init__.py b/burnman/minerals/__init__.py
index 1df557c..1bf7171 100644
--- a/burnman/minerals/__init__.py
+++ b/burnman/minerals/__init__.py
@@ -11,7 +11,6 @@ Mineral database
   - :mod:`~burnman.minerals.Murakami_etal_2012`
   - :mod:`~burnman.minerals.Murakami_2013`
   - :mod:`~burnman.minerals.Matas_etal_2007`
-  - :mod:`~burnman.minerals.HP_2011_fluids`
   - :mod:`~burnman.minerals.HP_2011_ds62`
   - :mod:`~burnman.minerals.HHPH_2013`
   - :mod:`~burnman.minerals.other`
diff --git a/burnman/solidsolution.py b/burnman/solidsolution.py
index 953a781..48c4951 100644
--- a/burnman/solidsolution.py
+++ b/burnman/solidsolution.py
@@ -3,13 +3,11 @@
 # Released under GPL v2 or later.
 
 import numpy as np
-from burnman.mineral import Mineral
-from burnman.processchemistry import ProcessSolidSolutionChemistry
-from burnman.solutionmodel import SolutionModel
-import constants
-import warnings
 
-kd = lambda x,y : 1 if x==y else 0
+from burnman import Mineral
+from solutionmodel import SolutionModel
+from solutionmodel import kd
+
 
 class SolidSolution(Mineral):
     """
@@ -27,19 +25,40 @@ class SolidSolution(Mineral):
     and P derivatives in J/K/mol and m^3/mol.
     """
 
-    # init sets up matrices to speed up calculations for when P, T, X is defined.
-    def __init__(self, base_material, solution_model = SolutionModel() ):
+    def __init__(self, endmembers, solution_model=SolutionModel()):
+        """
+        Set up matrices to speed up calculations for when P, T, X is defined.
+
+        Parameters
+        ----------
+        endmembers: list of :class:`burnman.Mineral`
+            List of endmembers in this solid solution.
+        solution_model: :class:`burnman.SolutionModel`
+            SolutionModel to use.
+        """
+
         # Initialise the solid solution inputs
-        self.base_material = base_material
+        self.base_material = endmembers
         self.solution_model = solution_model
 
         # Number of endmembers in the solid solution
-        self.n_endmembers=len(base_material)
+        self.n_endmembers = len(endmembers)
 
         for i in range(self.n_endmembers):
             self.base_material[i][0].set_method(self.base_material[i][0].params['equation_of_state'])
 
-    def set_composition( self, molar_fraction ):
+    def get_endmembers(self):
+        return self.base_material
+
+    def set_composition(self, molar_fraction ):
+        """
+        Set the composition for this solid solution.
+
+        Parameters
+        ----------
+        molar_fraction: list of float
+            molar abundance for each endmember, needs to sum to one.
+        """
         assert(len(self.base_material) == len(molar_fraction))
         assert(sum(molar_fraction) > 0.9999)
         assert(sum(molar_fraction) < 1.0001)
diff --git a/burnman/solutionmodel.py b/burnman/solutionmodel.py
index 152c1cc..e12dba3 100644
--- a/burnman/solutionmodel.py
+++ b/burnman/solutionmodel.py
@@ -8,8 +8,13 @@ import burnman
 from burnman.processchemistry import *
 import constants
 
-kd = lambda x,y : 1 if x==y else 0
-class SolutionModel:
+"""
+kronecker delta function for integers
+"""
+kd = lambda x, y: 1 if x == y else 0
+
+
+class SolutionModel(object):
     """
     This is the base class for a solution model,  intended for use
     in defining solid solutions and performing thermodynamic calculations
@@ -22,6 +27,12 @@ class SolutionModel:
     different endmember values.
     """
 
+    def __init__(self):
+        """
+        Does nothing.
+        """
+        pass
+
     def excess_gibbs_free_energy( self, pressure, temperature, molar_fractions):
         """
         Given a list of molar fractions of different phases,
@@ -97,7 +108,7 @@ class SolutionModel:
         return 0.0
 
 
-class IdealSolution ( SolutionModel ):
+class IdealSolution (SolutionModel):
     """
     A very simple class representing an ideal solution model.
     Calculate the excess gibbs free energy due to configurational
@@ -156,7 +167,6 @@ 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)
         activities=np.empty(shape=(self.n_endmembers))
@@ -171,7 +181,7 @@ class IdealSolution ( SolutionModel ):
         return activities
 
  
-class AsymmetricRegularSolution ( IdealSolution ):
+class AsymmetricRegularSolution (IdealSolution):
     """
     Solution model implementing the asymmetric regular solution model formulation (Holland and Powell, 2003)
     """
@@ -258,7 +268,8 @@ class AsymmetricRegularSolution ( IdealSolution ):
         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 )
 
-class SymmetricRegularSolution ( AsymmetricRegularSolution ):
+
+class SymmetricRegularSolution (AsymmetricRegularSolution):
     """
     Solution model implementing the symmetric regular solution model
     """
diff --git a/tests/test_eos.py b/tests/test_eos.py
index d118661..bf45d61 100644
--- a/tests/test_eos.py
+++ b/tests/test_eos.py
@@ -36,7 +36,7 @@ class eos(BurnManTest):
         rock = mypericlase()
         pressure = 0.
         temperature = 300.
-        eoses = [burnman.slb.SLB2(), burnman.slb.SLB3(), burnman.birch_murnaghan.BM2(), burnman.birch_murnaghan.BM3()]
+        eoses = [burnman.eos.SLB2(), burnman.eos.SLB3(), burnman.eos.BM2(), burnman.eos.BM3()]
 
         for i in eoses:
             Volume_test = i.volume(pressure, temperature, rock.params)
@@ -56,7 +56,7 @@ class eos(BurnManTest):
             Cv_test = i.heat_capacity_v(pressure, temperature, rock.params['V_0'], rock.params)
             Grun_test = i.grueneisen_parameter(pressure, temperature, rock.params['V_0'], rock.params)
 
-        eoses_thermal = [burnman.slb.SLB2(), burnman.slb.SLB3()]
+        eoses_thermal = [burnman.eos.SLB2(), burnman.eos.SLB3()]
         for i in eoses_thermal:
             Cp_test = i.heat_capacity_p(pressure, temperature, rock.params['V_0'], rock.params)
             self.assertFloatEqual(Cp_test, 37.076768469502042)