Merge branch 'master' of https://github.com/lordkman/burnman into Pla…

…nets

Readme.md

@@ -26,7 +26,7 @@ ian.rose@berkeley.edu
 
 ## Requirements
 
-* Python 2.7 (not Python 3.x)
+* Python 2.7.x or Python 3.4+
 * Python modules:
   NumPy, SciPy, Matplotlib
 
@@ -44,8 +44,8 @@ Figures should show up, indicating that it is working.
 
 1. get Xcode
 2. If you don't have Python yet, download it (for free) from
-   python.org/download . Make sure to use the latest version 2.x version (I
-   used 2.7). To check your version of python, type the following in a
+   python.org/download . Make sure to use either Python 2.7 or Python 3.4+.
+   To check your version of python, type the following in a
    terminal: 
      python --version
 3. Install the latest Numpy version: http://sourceforge.net/projects/numpy/files/NumPy/
@@ -72,7 +72,7 @@ python
 
 ## Install under Windows
 
-make Python 2.7.3 (for example) running under windows (do not use Python 3.x, but 2.7.x):
+To get Python 2.7.x (for example) running under Windows:
 
 1. Download Python from http://www.python.org/ and install the version at C:\Python27\; the 32-bit version is recommended
 2. Go to http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy, download "numpy-MKL-1.6.2.win32-py2.7.exe" and install
@@ -106,13 +106,13 @@ possible as well as each of the helpers involved with each example.
 Burnman has the advantage of being adaptable and extendable in easy scripts. The downside might be that we do not
 provide a graphical user interface. For those of you who are not familiar  with python, we suspect it will still be 
 relatively easy to adapt the scripts for computations and plotting. 
-Here are some specific features and pitfalls on python:
+Here are some specific features and pitfalls on Python:
 
 * Python uses specific identation. A script might fail if a code block is not idented correctly. We use four spaces and no tabs, 
   mixing these can give trouble.
 * Indices require square brackets and function or method calls parentheses (mainly different from Matlab).
 * The first index of an array is 0 (e.g. x[0])
-* Put dots after numbers to make them floats instead of integers (e.g. 5/3 will give 1 (rounded downward), while 5./3. will give 1.66666666667)
+* Put dots after numbers to make them floats instead of integers (e.g. 5/3 will give 1 (Python 2.x rounds downward), while 5./3. will give 1.66666666667)
 
 
 ## Examples 

burnman/__init__.py

@@ -54,34 +54,35 @@
     Bill McDonough, Quentin Williams, Wendy Panero, and Wolfgang Bangerth.
 
 """
+from __future__ import absolute_import
 
-from version import version as __version__
+from .version import version as __version__
 
 # classes for representing rocks and minerals:
-from mineral import Mineral
-from material import Material
-from composite import Composite
-from solutionmodel import SolutionModel
-from solidsolution import SolidSolution
-from mineral_helpers import *
+from .mineral import Mineral
+from .material import Material
+from .composite import Composite
+from .solutionmodel import SolutionModel
+from .solidsolution import SolidSolution
+from .mineral_helpers import *
 
 # high level functions
-from main import *
-from model import Model
+from .main import *
+from .model import Model
 
 # mineral library
-import minerals
+from . import minerals
 
 # central user tools
-import seismic
-import averaging_schemes
-import eos
+from . import seismic
+from . import averaging_schemes
+from . import eos
 
-import processchemistry
-import chemicalpotentials
-from solutionmodel import SolutionModel
-import geotherm
+from . import processchemistry
+from . import chemicalpotentials
+from .solutionmodel import SolutionModel
+from . import geotherm
 
 # miscellaneous
-import tools
-from partitioning import calculate_partition_coefficient,calculate_phase_percents
+from . import tools
+from .partitioning import calculate_partition_coefficient,calculate_phase_percents

burnman/averaging_schemes.py

@@ -1,7 +1,7 @@
 # This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
 # Copyright (C) 2012 - 2015 by the BurnMan team, released under the GNU GPL v2 or later.
 
-
+from __future__ import absolute_import
 import numpy as np
 import warnings
 
@@ -64,8 +64,7 @@ def average_shear_moduli(self, volumes, bulk_moduli, shear_moduli):
     def average_density(self, volumes, densities):
         """
         Average the densities of a composite, given a list of volume
-        fractions and densitites. This is the only method of
-        :class:`burnman.averaging_schemes.AveragingScheme` which is implemented in the base class,
+        fractions and densitites. This is implemented in the base class,
         as how to calculate it is not dependent on the geometry of the rock.
         The formula for density is given by
 
@@ -559,10 +558,8 @@ def voigt_average_function(phase_volume, X):
     voigt_reuss_hill classes, takes a list of
     volumes and moduli, returns a modulus.
     """
-    it = range(len(phase_volume))
-    V_i = phase_volume
-    V_tot = sum(V_i)
-    X_voigt = sum(V_i[i]/V_tot * X[i] for i in it)
+    vol_frac = phase_volume/np.sum(phase_volume)
+    X_voigt = sum( f*x for f,x in zip(vol_frac, X))
     return X_voigt
 
 
@@ -573,14 +570,12 @@ def reuss_average_function(phase_volume, X):
     voigt_reuss_hill classes, takes a list of
     volumes and moduli, returns a modulus.
     """
-    it = range(len(phase_volume))
-    V_i = phase_volume
-    V_tot = sum(V_i)
-    if (min(X)<=0.0):
-        X_reuss = 0.0
-        warnings.warn("Oops, called reuss_average with Xi<=0!")
-    else:
-        X_reuss = 1./sum(V_i[i]/V_tot* 1./X[i] for i in it)
+    vol_frac = phase_volume/np.sum(phase_volume)
+    for f,x in zip(vol_frac,X):
+        if x <= 0 and np.abs(f) > np.finfo(float).eps :
+            warnings.warn("Oops, called reuss_average with Xi<=0!")
+            return 0.0
+    X_reuss = 1./sum( f/x for f,x in zip(vol_frac, X))
     return X_reuss
 
 

burnman/chemicalpotentials.py

@@ -1,14 +1,13 @@
 # This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
 # Copyright (C) 2012 - 2015 by the BurnMan team, released under the GNU GPL v2 or later.
 
-
+from __future__ import absolute_import
 import numpy as np
 from scipy.linalg import lu
 
-import burnman
-from burnman import minerals
-from processchemistry import *
-import burnman.constants as constants
+from .processchemistry import *
+from . import constants
+from . import solidsolution
 
 # This module computes chemical potentials (partial molar gibbs free energies) for an assemblage based on the Gibbs free energies and compositions of the individual phases.
 
@@ -48,7 +47,7 @@ def chemical_potentials(assemblage, component_formulae):
     endmember_list=[]
     endmember_potentials=[]
     for mineral in assemblage:
-        if isinstance(mineral, burnman.SolidSolution):
+        if isinstance(mineral, solidsolution.SolidSolution):
             for member in mineral.endmembers:
                 endmember_list.append(member[0])
             for potential in mineral.partial_gibbs: