[cig-commits] [commit] add_thermodynamic_potentials's head updated: Move things around (d5ddad0)

[cig_noreply at geodynamics.org]

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

Branch 'add_thermodynamic_potentials' now includes:

     e11c770 Use scipy.constants for physical constants.
     d9ae13d fix test output
     d0894c8 tests: better float comparisons
     ac2c35d update tests to use new floating point check
     4632238 remove annoying output
     7b0e5a7 use numdiff
     a1bfc7b Add a burnman.constants file to import the scipy constants
     d4a0004 Merge pull request #39 from ian-r-rose/offload_constants
     7ba368b Initial working copy (non-functional) adding solid solutions
     5b03886 Adding non-functional solidsolution.py
     ca277f4 Abbreviate kd
     94d8bac Add Modified Tait EoS and expression for G
     9dcbc7b Added molar mass calculator and data table
     2dff620 Minor corrections
     cdb8c44 Added endmember Gibbs with Landau, and a new test script.
     3bbd979 Started work on Bragg-Williams order-disorder.
     ec1fd6d Continued work on Bragg-Williams order-disorder.
     a88fd04 Added minerals to HP_2011.py
     9f037a6 Attempts to locate tc-burnman discrepancies
     0241963 Implemented HP2011 Landau and Bragg-Williams order-disorder models for endmembers
     d7ffcf3 Added HP2011 ds62 and associated parser
     c28b11f Added Katsura_2009_wadsleyite
     e10f600 Added comment to warn that Cp, V where Landau/Bragg-Williams order-disorder is implemented are currently incorrect
     5d26be8 Added preliminary format for SolidSolution parameters
     f47e82f Added pv SolidSolution parameters
     eb13f4d Minor edit
     777fd1d Implemented sample_pressure attribute for experimental data inversion
     729c545 Added TO_DO_LIST.txt
     eac9b33 Added start of test script to process solid solution models
     efbf2b7 Moved HP2011 test to tests directory
     69d3701 Add interface for thermodynamic potentials
     1c3ca5a Update name of gibbs function
     618ce37 Add einstein thermal model
     30679c0 Use einstein.py to do the heat capacity stuff, implement a few of the not-yet-completed thermodynamic functions
     920e093 Remove unnecessary inheritance
     c6b4ada SolidSolution test now includes site occupancies and ideal activities
     97cb077 Bugfixes
     d778449 Corrected HP2011 data parsing
     ed81e69 Corrected HP2011 data parsing
     1703b69 Corrected HP2011 data parsing
     feef42b Make work
     3f65428 Added print statements for module addition to HPdata parsing
     8880b18 Add the ability to calculate Helmholtz and Gibbs free energies to SLB, and more generally to anything using the Debye model.
     feb9540 Remove already inherited methods
     394dcc2 Calculate Gibbs and Helmholtz in the mineral class, but fail silently if they are not implemented/unable.
     0540640 Added non-ideal contribution to solidsolution test file
     a073d79 Minor change
     899eb1e Comments added to test_process_solidsolution.py
     e7001f9 Minor change
     e264d07 Added excess S, V to test_process_solidsolution.py
     8a557c9 Added example plot to test_process_solidsolution.py
     8c5e99f First alpha of SolidSolution base class
     7fbd0e4 Corrected sign of S excess
     aaf4bc4 Added configurational entropy to solidsolution.py
     d3f22ef Created test code for solidsolution models
     db2891a Removed superseded SLB_2011_working.py
     9b4e788 Commented ds62 input file
     f7d865d Commented ds62 input file
     f2ca154 Rename to emphasize extensive quantity
     a8e6042 Added more attributes to the solidsolution class
     0cbfa49 Rejigged SolidSolution class
     29bb7a5 Added check for endmember and solid solution member compositional equality
     ee33dd1 Added solid solutions from hefesto to new SLB_2011 input file
     e4a5ba1 Documented and changed name of sample_pressure (now eos_pressure)
     0bf0815 Re-removed comments in mineral classes
     67bc3e7 Moved molar_mass.py to misc/
     df86cd4 Changed comment blob for burnman.SolidSolution
     9a6bc82 Solid solutions in SLB2011 given full names and abbreviated aliases
     29f9f4b Prepped new SLB2011 input file to take all the endmembers in SLB2011
     aff4977 Add pressure to the various EOSs that need it
     0cb6de4 Centralised and dictionarised formula parsing
     178268b Bug fixes
     f3b6439 Initial version of SolutionModel class, including one that does nothing, and IdealSolution class, a SymmetricVanLaar class, and an AsymmetricVanLaar class.  Still work to be done
     76690db Add missing file
     a1474c9 Rename classes
     43bbef9 Commented functions in processchemistry.py
     6328247 Started benchmarking document to test solid solutions
     03872c9 Patch up so that the new stuff works as a package
     eac6fce Bug fixes
     0d331f8 Move out of burnman directory
     ae5fb79 Add the enthalpy of solution benchmark
     65b5223 Added compositional array construction
     9efbcdc Split configurational entropy from ideal gibbs
     78cf89e Minor bug fix
     9ac0935 Added chemicalpotentials stub
     6fe76aa Fix typos
     effb648 Start trying to do configurational entropy benchmark
     6acdd08 Bugfix
     ea5b24c Reproduce two of the curves from fig 3b
     1f4fc6c Use np.power
     d3bdf15 Temporary fix until ProcessSolidSolutionChemistry is fixed
     0219d63 Bug fix for formula parsing
     fb00f85 Another bug fix for processchemistry.py
     f7f2f98 Remove unnecessary ones.
     5ef1a29 Added chemical potential and fugacity functions and examples
     a3d49d1 Variable change to ease comparison with diagram
     a4dc8be Implemented endmember configurational entropies for disordered phases
     d13f83f Overlay screengrabs
     8cc2237 Add another configurational entropy example
     2ef7aa9 Simplified configurational entropy calculation
     ea6d8de Finished ideal activity formulation
     d702f2c Changed zero equality for endmember occupancy to tolerance
     177117b Widened compositional bounds on spinel entropy benchmark
     ca069d7 Added comment for origin of formula in benchmark
     f122e0f Parsed SLB_2011 endmembers into data file
     0fa8e10 Merged SLB_2011.py with solid-solution-bearing file
     132e1f2 Updated TO_DO_LIST.txt
     3de86f8 Fix things, change to SI
     e8ef8c7 Bugfix
     dc69656 Restored aliases to SLB_2011.py
     6f5b574 Fix broken aliases
     a4109be Tweaked axes in solidsolution benchmarks
     e692ab9 Emphasised the physical meaning of the normalisation constant in activity calculations
     39ef045 Adapted gibbs and chemical potential processing
     c7f9303 Added CORK equation of state and benchmarks
     8cd22e2 Added preliminary metal-metal oxide buffer data
     b53d7d1 Updated to do list
     9aa9291 Added Re-ReO2 buffer to test_chemical_potentials example
     4ef26ce Add code fragments from thermopy to help with gibbs minimization
     87d7702 Fixed Gibbs bug created last night
     23f5a51 Removed pressure as input variable to F(V,T) and volume as input variable to Gibbs(P,T)
     fd15837 Added Holland et al., 2013 lower mantle dataset
     ee44b8c Added parsers for Holland et al., 2013 data table
     36b750b Minor bug fix
     cadd5b5 Added P,T attributes and calcgibbs to solid solution class
     e7b24d1 Start working on a gibbs minimization branch
     269fc2c More work on gibbs minimization.  Not remotely working
     655901b More work on setting up the gibbs minimization problem
     bcce302 More scattered work
     cc6b47d More disorganized work
     f1b69f5 Bugfix
     6002e6b Add a bunch of documentation
     4f5cce6 Cleanup.
     8e00ae3 Documentation dump
     66eca0c Remove unused imports
     757cd70 Allow multiple instances of same element in endmember formulae
     b840571 Bugfix
     57e145b Add test script. Not working
     9d2ff0f Added tc test
     833d921 Bugfix for entropy term in ideal_gibbs_excess, added partial gibbs functions
     d1d528f Added set_method to solid solution initialisation, added partial gibbs function
     897f9c5 Added temporary test for previously buggy gibbs excesses
     4451e82 Added alpha version of tc-like equilibrium assemblage calculations
     d5ddad0 Move things around