Merge pull request reaktoro#196 from allanleal/py-eq-inv-solver

Implement python wrapper for EquilibriumInverseSolver

Fix CondaAware and memory leak in ChemicalQuantity (reaktoro#175)

* Don't let CondaAware mess with python if PYTHON_EXECUTABLE is specified

* Solve memory leak in ChemicalQuantity

Authored-by: Allan Leal

fixed unit of element molar mass when using ThermoFun (reaktoro#174)

* fixed unit for elements to SI when using thermofun

* updated thermofun regression tests data

Update regression test data

Pin ThermoFun to version 0.3.3

Thermofun integration (reaktoro#95)

* Enhanced units with additional entries commonly used in geochemistry

* Changes to units after pull request comments

* Fix alignment of commas

* Update Units.cpp

* Using mc only for common cases (see description)

Using `mc` only for the following cases (which are more common):

- mcg
- mcmol
- mcl
- mcL
- mcmolal
- mcmolar
- mceq

* started changes for thermofun integration

* added first test database file in thermohub format

* added thermofun thirdparty lib dependency /usr/local/

* finished first attempt at thermofun integration, needs testing

* added ChemmicalEditor constructor using ThermoFun::Database, plus bugfix

* added demo for using ThermoFun thermodynamic backend

* supcrt07 database in thermofun format

* fixes for ThermoFun lib name change

* fixed ThermoFun include to new naming

* Update Reaktoro/Thermodynamics/Core/Thermo.cpp

Co-Authored-By: Allan Leal <[email protected]>

* Fix build issue

* ThermoFun has public dependency

* Increase temperature and pressure interpolation points by default

* Remove command to link demos against ThermoFun manually

* Add some time measurements

* Fixed condition to call ThermoFun

* Output time of initialization, properties calculations, comparison with direct ThemroFun calculations

* fixed to previous T-P interoplation list, this T-P list is not used in ThermoFun integration

* more detailed intitialization, solving, TFun calculation, time comparison

* Update ChemicalEditor.cpp

* changed the ChemicalEditor ThermoFun constructor, made separate default function for setting interpolation T-P grid

* removed commented out code

* removed commented out code

* Update Reaktoro/Thermodynamics/Core/Thermo.cpp

Co-Authored-By: Allan Leal <[email protected]>

* Fix build issue

* ThermoFun has public dependency

* Increase temperature and pressure interpolation points by default

* Remove command to link demos against ThermoFun manually

* Add some time measurements

* Fixed condition to call ThermoFun

* Output time of initialization, properties calculations, comparison with direct ThemroFun calculations

* fixed to previous T-P interoplation list, this T-P list is not used in ThermoFun integration

* more detailed intitialization, solving, TFun calculation, time comparison

* Enable Travis CI for macOS (reaktoro#88)

* Enable Travis CI for macOS

* Fix issue reaktoro#91

* Remove assumption that a locale with comma for decimas is available.

This fails in my machine, since there is no locale here that represent decimal with comma.

* Add missing approx(...))

* Regenerate pytest-regression data

* Remove element potentials and add gibbs energy

* Fix regression failures due to element dual potentials

* Normalizing Gibbs energy in regression tests

* Increased relative tolerance to 1e-14 (was 1e-16)

* Add missing tol params

* Add precision and fix output spacing

* Add precision to output of equilibrium/kinetic paths

* Fix tests

* Add missing cmath header

* Fix chck of nan on Temperature and Pressure

* Several improvements

* Add abstol

* Exlude pH when checking approximate result

* Fix exclude bug

* Add macOS support in check_compiled_files.py script

* Add CMake improvements related to Debug builds

 * Fix Debug build in AppVeyor to really be a debug build
 * Improve CMake to install debug symbols (.pdb files)
 * Improve parameter passing to third-party libraries CMake builds (when in Debug and in Windows)
 * Add support (flag) for a more verbose build

* Change to use MSVC 2017 in Windows (reaktoro#103)

* EquilibriumSolver::solve fails with an EquilibriumProblem that has inert elements (reaktoro#102)

- add test for EquilibriumSolver and treat inert elements inside it

* Fix issue reaktoro#91 (reaktoro#93)

* Fix issue reaktoro#91

* Remove assumption that a locale with comma for decimas is available.

This fails in my machine, since there is no locale here that represent decimal with comma.

* Add missing approx(...))

* Regenerate pytest-regression data

* Remove element potentials and add gibbs energy

* Fix regression failures due to element dual potentials

* Normalizing Gibbs energy in regression tests

* Increased relative tolerance to 1e-14 (was 1e-16)

* Add missing tol params

* Add precision and fix output spacing

* Add precision to output of equilibrium/kinetic paths

* Fix tests

* Add python bindings for ThermoData and tests and add support for C++17 (reaktoro#99)

* Update ChemicalEditor.cpp

* changed the ChemicalEditor ThermoFun constructor, made separate default function for setting interpolation T-P grid

* removed commented out code

* removed commented out code

* added ThermoFun integration to reaktoro python binding

* added thermofun integration test for python

* slo98 database in thermohub json format for using with thermofun

* new database format

* added new tfun simplified database format

* refreshed thermofun databases

* Organize a few things on the integration.

* Add regression tests for thermofun+reaktoro integration

* requested changes, removed commented code, added assert for not valid species, constructor with thermofun database now explicit

* Remove aq17-fun.json in favor of aq17-thermofun.json

* Add REQUIRED back to find_package ThermoFun

* Add missing doc for new constructor.

* Add explicit for constructor Database(ThermoFun::Database)

Fix mac build pybind11 issue (reaktoro#125)

* Add clangcxx=9.0.0 as a new deps

* Fix clang-9 error when using C++17 and pybind11

* Add -fno-sized-deallocation when using clang-9

Upgrade eigen to latest dev version and add /Zc:__cplusplus compiler …

…option (reaktoro#121)

* Update eigen3 with latest dev version

* Remove eigen matrix plugin (not needed anymore)

* Regenerate regression test data files with slightly small differences now that a new eigen version is used

* Add /Zc:__cplusplus to list of compile options for MSVC

Fix missing propagation of CXX17 requirement to dependent codes (reak…

…toro#109)

* Move CXX17 compilation feature to Reaktoro target.

This is a more cmake modern way of doing things (by assiging properties to the targets).

* Fix cmake demo

* Fix division by zero in ChemicalProperties::update

* Ensure pybind11 really used c++17

* Add fPIC back

In PyMineralReaction.cpp, added setSurfaceArea-python-binding. (reakt…

…oro#84)