[cig-commits] [commit] doc_updates: Changes to doocumentation to incorporate new thermodynamics stuff. (4e11d05)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Mon Dec 29 10:54:26 PST 2014
Repository : https://github.com/geodynamics/burnman
On branch : doc_updates
Link : https://github.com/geodynamics/burnman/compare/0000000000000000000000000000000000000000...4e11d0554608423ba62477616416f6990d18cf23
>---------------------------------------------------------------
commit 4e11d0554608423ba62477616416f6990d18cf23
Author: ian-r-rose <ian.r.rose at gmail.com>
Date: Mon Dec 29 10:53:38 2014 -0800
Changes to doocumentation to incorporate new thermodynamics stuff.
>---------------------------------------------------------------
4e11d0554608423ba62477616416f6990d18cf23
burnman/__init__.py | 1 +
burnman/eos/slb.py | 2 +-
burnman/mineral_helpers.py | 4 ++++
burnman/solidsolution.py | 4 +++-
burnman/solutionmodel.py | 4 +++-
sphinx/background.rst | 2 +-
sphinx/eos.rst | 13 +++++++++++--
sphinx/index.rst | 5 +++--
sphinx/{minerals.rst => materials.rst} | 33 ++++++++++++++-------------------
9 files changed, 41 insertions(+), 27 deletions(-)
diff --git a/burnman/__init__.py b/burnman/__init__.py
index 583e3c5..b1980d9 100644
--- a/burnman/__init__.py
+++ b/burnman/__init__.py
@@ -71,6 +71,7 @@ import averaging_schemes
import eos
import processchemistry
+import chemicalpotentials
from solutionmodel import SolutionModel
import geotherm
diff --git a/burnman/eos/slb.py b/burnman/eos/slb.py
index 5186121..52102cc 100644
--- a/burnman/eos/slb.py
+++ b/burnman/eos/slb.py
@@ -306,7 +306,7 @@ class SLB3(SLBBase):
"""
SLB equation of state with third order finite strain expansion for the
shear modulus (this should be preferred, as it is more thermodynamically
- consistent.
+ consistent.)
"""
def __init__(self):
self.order=3
diff --git a/burnman/mineral_helpers.py b/burnman/mineral_helpers.py
index 81c68ed..4437c2b 100644
--- a/burnman/mineral_helpers.py
+++ b/burnman/mineral_helpers.py
@@ -21,6 +21,8 @@ from burnman import Material, Mineral
class HelperSolidSolution(Mineral):
"""
+ This material is deprecated!
+
Class for coming up with a new mineral based based on a solid
solution between two or more end member minerals. It is not
completely clear how to do this, or how valid this approximation
@@ -128,6 +130,8 @@ class HelperSpinTransition(Material):
class HelperFeDependent(Material):
"""
+ This material is deprecated!
+
Helper to implement a rock that does iron exchange (two minerals with
changing iron content based on P,T).
diff --git a/burnman/solidsolution.py b/burnman/solidsolution.py
index cee8daf..3741081 100644
--- a/burnman/solidsolution.py
+++ b/burnman/solidsolution.py
@@ -18,7 +18,9 @@ class SolidSolution(Mineral):
States of the solid solution can only be queried after setting
the pressure, temperature and composition using set_state().
- This class is available as ``burnman.SolidSolution``.
+ This class is available as :class:`burnman.SolidSolution`.
+ It uses an instance of :class:`burnman.SolutionModel` to
+ calculate interaction terms between endmembers.
All the solid solution parameters are expected to be in SI units. This
means that the interaction parameters should be in J/mol, with the T
diff --git a/burnman/solutionmodel.py b/burnman/solutionmodel.py
index 30d4d5f..390cede 100644
--- a/burnman/solutionmodel.py
+++ b/burnman/solutionmodel.py
@@ -18,7 +18,9 @@ class SolutionModel(object):
"""
This is the base class for a solution model, intended for use
in defining solid solutions and performing thermodynamic calculations
- on them.
+ on them. All minerals of type :class:`burnman.SolidSolution` use
+ a solution model for defining how the endmembers in the solid solution
+ interact.
A user wanting a new solution model should define the functions for
excess_gibbs_free_energy and excess_volume. In the base class these
diff --git a/sphinx/background.rst b/sphinx/background.rst
index a46907d..3cd068f 100644
--- a/sphinx/background.rst
+++ b/sphinx/background.rst
@@ -398,7 +398,7 @@ One can choose to evaluate :math:`V_P, V_\Phi, V_S, \rho, K_S` and/or :math:`G`.
The user can input their own seismic profile, an example of which is included using AK135 :cite:`Kennett1995`.
Besides standardized 1D radial profiles, one can also compare to regionalized average profiles for the lower mantle.
-This option accommodates the observation that the lowermost mantle can be clustered into two regions, a 'slow' region, which represents the so-called Large Low Shear Velocity Provinces, and 'fast' region, the continuous surrounding region where slabs might subduct :cite:`lekic2012`.
+This option accommodates the observation that the lowermost mantle can be clustered into two regions, a 'slow' region, which represents the so-called Large Low Shear Velocity Provinces, and 'fast' region, the continuous surrounding region where slabs might subduct :cite:`Lekic2012`.
This clustering as well as the averaging of the 1D model occurs over five tomographic S wave velocity models (SAW24B16: :cite:`megnin2000`; HMSL-S: :cite:`houser2008`; S362ANI: :cite:`Kustowski2008`; GyPSuM: :cite:`Simmons2010`; S40RTS: :cite:`Ritsema2011`).
The strongest deviations from PREM occur in the lowermost 1000 km.
Using the 'fast' and 'slow' S wave velocity profiles is therefore most important when interpreting the lowermost mantle. Suggestion of compositional variation between these regions comes from seismology :cite:`to2005,He2012` as well as geochemistry :cite:`Deschamps2012,jackson2010`.
diff --git a/sphinx/eos.rst b/sphinx/eos.rst
index 8c8d962..b5c85e2 100644
--- a/sphinx/eos.rst
+++ b/sphinx/eos.rst
@@ -8,7 +8,7 @@ Base class
Birch-Murnaghan
---------------
-.. autoclass:: burnman.eos.BirchMurnaghanBase
+.. autoclass:: burnman.eos.birch_murnaghan.BirchMurnaghanBase
.. autoclass:: burnman.eos.BM2
@@ -17,12 +17,21 @@ Birch-Murnaghan
Stixrude and Lithgow-Bertelloni Formulation
-------------------------------------------
-.. autoclass:: burnman.eos.SLBBase
+.. autoclass:: burnman.eos.slb.SLBBase
.. autoclass:: burnman.eos.SLB2
.. autoclass:: burnman.eos.SLB3
+Mie-Grüneisen-Debye
+-------------------------------------------
+
+.. autoclass:: burnman.eos.mie_grueneisen_debye.MGDBase
+
+.. autoclass:: burnman.eos.MGD2
+
+.. autoclass:: burnman.eos.MGD3
+
Modified Tait
-------------
.. autoclass:: burnman.eos.MT
diff --git a/sphinx/index.rst b/sphinx/index.rst
index 0ca7132..9493637 100644
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -15,15 +15,16 @@ Welcome to BurnMan's documentation!
background
examples
main
+ materials
eos
averaging
+ thermodynamics
geotherms
- minerals
seismic
mineral_database
zreferences
-The functions in the :doc:`main` operate on :doc:`minerals` which can be
+The functions in the :doc:`main` operate on :doc:`materials` which can be
combination of different minerals from :doc:`mineral_database`.
diff --git a/sphinx/minerals.rst b/sphinx/materials.rst
similarity index 50%
rename from sphinx/minerals.rst
rename to sphinx/materials.rst
index 54dbd74..dd30b46 100644
--- a/sphinx/minerals.rst
+++ b/sphinx/materials.rst
@@ -1,39 +1,34 @@
-Minerals
-========
+Materials
+=========
-Burnman operates on rocks (type :class:`~burnman.material.Material`) most prominently in form of minerals (:class:`~burnman.mineral.Mineral`) and composites (:class:`~burnman.composite.Composite`).
+Burnman operates on materials (type :class:`~burnman.material.Material`) most prominently in form of minerals (:class:`~burnman.mineral.Mineral`) and composites (:class:`~burnman.composite.Composite`).
-.. inheritance-diagram:: burnman.Material burnman.Composite burnman.Mineral burnman.mineral_helpers.HelperSolidSolution burnman.mineral_helpers.HelperSpinTransition burnman.mineral_helpers.HelperFeDependent
+.. inheritance-diagram:: burnman.Material burnman.Composite burnman.Mineral burnman.solidsolution.SolidSolution burnman.mineral_helpers.HelperSpinTransition
-Base Class
-----------
+Base Material
+-------------
.. autoclass:: burnman.material.Material
-Base for individual Minerals
+Minerals
----------------------------
-
.. autoclass:: burnman.mineral.Mineral
-Composite
----------
-
-.. autoclass:: burnman.composite.Composite
+.. autoclass:: burnman.SolidSolution
+.. autoclass:: burnman.mineral_helpers.HelperSpinTransition
+.. autoclass:: burnman.mineral_helpers.HelperSolidSolution
+.. autoclass:: burnman.mineral_helpers.HelperFeDependent
-Mineral helpers
----------------
+Composite
+---------
-.. autoclass:: burnman.SolidSolution
-.. autoclass:: burnman.SolutionModel
-.. autoclass:: burnman.mineral_helpers.HelperSpinTransition
-.. autoclass:: burnman.mineral_helpers.HelperSolidSolution
-.. autoclass:: burnman.mineral_helpers.HelperFeDependent
+.. autoclass:: burnman.composite.Composite
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