diff --git a/CMakeLists.txt b/CMakeLists.txt
index 751f460..8f90787 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,255 +1,246 @@
####################################################
# #
# SpecMiCP : CMakeLists.txt #
# #
####################################################
project(specmicp)
cmake_minimum_required(VERSION 2.8.8)
# Configuration options
# ======================
# For an explanation of the options see the INSTALL file
option(SPECMICP_USE_OPENMP "Thread parallelisation of specmicp instances if available" ON)
option(SPECMICP_NO_DEBUG "Disable SpecMiCP assert" OFF)
option(SPECMICP_BUILD_STATIC "Build static libraries" OFF)
option(SPECMICP_BUILD_EXAMPLE "Build the examples" ON)
-option(SPECMICP_BUILD_CYTHON "Build the cython module" ON)
option(SPECMICP_DEBUG_EQUATION_FD_JACOBIAN "Use a finite difference jacobian is specmicp" OFF)
# PGO sequence
option(SPECMICP_PROFILE_GENERATE "Generate the profile for PGO optimization" OFF)
option(SPECMICP_PROFILE_USE "Use the generated profile for PGO optimization" OFF)
# global variables
# ================
set(SPECMICP_VERSION 0.0.3)
# External Package
# ================
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake)
# OpenMP
#-------
# not required but recommended
if(SPECMICP_USE_OPENMP)
find_package(OpenMP)
endif()
# Boost
# -----
find_package(Boost REQUIRED)
include_directories(${Boost_INCLUDE_DIR})
# Eigen
# -----
find_package(Eigen3 REQUIRED) # This module comes from the Eigen3 Package
include_directories(${EIGEN3_INCLUDE_DIR})
# Eigen unsuported
# GMRES.h is really the file we are using/looking for
# If it doesn't exist then the solver will not be included in the list of the parse solvers
if(EXISTS "${EIGEN3_INCLUDE_DIR}/unsupported/Eigen/src/IterativeSolvers/GMRES.h")
add_definitions(-DEIGEN_UNSUPPORTED_FOUND)
INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}/unsupported/")
endif()
add_custom_target(cmake_incl SOURCES cmake/FindSpecMiCP.cmake)
# sanitizer
include(SanitizerBuild)
# compilation flags
# =================
# c++11
# -----
include(CheckCXXCompilerFlag)
if(NOT CX11_FLAG)
check_cxx_compiler_flag("-std=c++11" HAS_CXX11)
if(NOT HAS_CXX11)
message(FATAL_ERROR "A c++11 compatible compiler is necessary")
else()
set(CXX11_FLAG "-std=c++11")
endif()
endif()
# -fvisibility=hidden
# ---------------------
# check if the compiler supports it
check_cxx_compiler_flag("-fvisibility=hidden" HAS_VISIBILITY_HIDDEN)
# define a set of files to be compiled with the -fvisibility=hidden flag
macro(set_visibility_hidden_flag)
if (HAS_VISIBILITY_HIDDEN)
foreach(file ${ARGN})
set_source_files_properties(${file} PROPERTIES COMPILE_FLAGS -fvisibility=hidden)
endforeach()
endif()
endmacro()
file(COPY pgo_sequence.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
file(COPY reactmicp.qsub DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
if(CMAKE_COMPILER_IS_GNUCXX)
if(SPECMICP_PROFILE_GENERATE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-generate")
if (SPECMICP_USE_OPENMP AND OPENMP_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-correction")
endif()
endif()
if(SPECMICP_PROFILE_USE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-use -Wno-error=coverage-mismatch")
if (SPECMICP_USE_OPENMP AND OPENMP_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-correction")
endif()
endif()
endif()
if(UNIX)
# Use ld.gold if it is available and isn't disabled explicitly
# Ref : https://bugs.webkit.org/show_bug.cgi?id=137953
if(CMAKE_COMPILER_IS_GNUCXX)
option(USE_LD_GOLD "Use GNU gold linker" ON)
if (USE_LD_GOLD)
execute_process(COMMAND ${CMAKE_C_COMPILER} -fuse-ld=gold -Wl,--version ERROR_QUIET OUTPUT_VARIABLE LD_VERSION)
if ("${LD_VERSION}" MATCHES "GNU gold")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fuse-ld=gold")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fuse-ld=gold")
else ()
message(WARNING "GNU gold linker isn't available, using the default system linker.")
endif ()
endif ()
endif()
# Generic options
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX11_FLAG}")
if (OPENMP_FOUND)
SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
##SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
message(STATUS "c++ flags ${CMAKE_CXX_FLAGS}")
else()
message(WARNING "not tested !")
endif()
# Directories
#########################################################################
# 3rd party
# =========
# JsonCPP
# -------
set(JSONCPP_DIR ${PROJECT_SOURCE_DIR}/3rdparty/jsoncpp/)
add_custom_target(3rdparty_header SOURCES
${JSONCPP_DIR}/json/json.h
${JSONCPP_DIR}/json/json-forwards.h
)
include_directories(${JSONCPP_DIR})
# installation dir
# ----------------
# http://www.cmake.org/pipermail/cmake/2010-February/035466.html
# compute default library install dir
if(UNIX)
# library
# ------
set (_DEFAULT_LIBRARY_INSTALL_DIR lib)
if (EXISTS "${CMAKE_INSTALL_PREFIX}/lib32/" AND CMAKE_SIZEOF_VOID_P EQUAL 4)
set (_DEFAULT_LIBRARY_INSTALL_DIR lib32)
elif (EXISTS "${CMAKE_INSTALL_PREFIX}/lib64/" AND CMAKE_SIZEOF_VOID_P EQUAL 8)
set (_DEFAULT_LIBRARY_INSTALL_DIR lib64)
endif ()
# the library install dir
set(LIBRARY_INSTALL_DIR "${_DEFAULT_LIBRARY_INSTALL_DIR}" CACHE PATH "Installation directory for libraries")
set(STATIC_LIBRARY_INSTALL_DIR "${_DEFAULT_LIBRARY_INSTALL_DIR}/static" CACHE PATH "Installation directory for static libraries")
# make the library install dir an absolute path (can be important e.g. when using CONFIGURE_FILE to embed
# the library installation directory into a file)
if(NOT IS_ABSOLUTE "${LIBRARY_INSTALL_DIR}")
set(LIBRARY_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${LIBRARY_INSTALL_DIR}")
endif()
if(NOT IS_ABSOLUTE "${STATIC_LIBRARY_INSTALL_DIR}")
set(STATIC_LIBRARY_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${STATIC_LIBRARY_INSTALL_DIR}")
endif()
# include
#--------
set(INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include/specmicp")
# share
#------
set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/share/specmicp")
else()
message(WARNING "not tested !")
endif()
enable_testing(true)
# CPP API : SpecMiCP / ReactMiCP
#########################################################################
# the main source directory - the c++ api
set(SPECMICP_CPP_API ${CMAKE_CURRENT_SOURCE_DIR}/src)
include_directories(${SPECMICP_CPP_API})
add_subdirectory( ${SPECMICP_CPP_API} )
# Database
#########################################################################
add_subdirectory( data )
# Documentation
#########################################################################
# "common" documentation
# -----------------------
set(
DOCS_LIST
${CMAKE_CURRENT_SOURCE_DIR}/README.md
${CMAKE_CURRENT_SOURCE_DIR}/INSTALL
${CMAKE_CURRENT_SOURCE_DIR}/COPYING
)
add_custom_target(docs SOURCES ${DOCS_LIST})
install(FILES ${DOCS_LIST}
DESTINATION ${SHARE_INSTALL_DIR}
)
install(FILES reactmicp.qsub
DESTINATION ${SHARE_INSTALL_DIR}
)
# Doxygen documentation
# ---------------------
add_subdirectory( doc )
# the cmake find module
# ---------------------
install(FILES cmake/FindSpecMiCP.cmake
DESTINATION ${SHARE_INSTALL_DIR}/cmake
)
-# The following modules have their own CMakeLists.txt
-
-# Python interface
-#########################################################################
-if (SPECMICP_BUILD_CYTHON)
- add_subdirectory( cython )
-endif()
-
# Tests
#########################################################################
add_subdirectory( tests )
# Examples
#########################################################################
add_subdirectory( examples )
diff --git a/INSTALL b/INSTALL
index 805a411..0a06ac3 100644
--- a/INSTALL
+++ b/INSTALL
@@ -1,93 +1,87 @@
Building SpecMiCP
-----------------
SpecMiCP uses CMake[1] as build system, to build it, in the specmicp directory, run :
cmake .
make
To customize build, see the cmake documentation[2] and the following informations :
Requirements :
==============
- C++11 compiler (tested with gcc 4.8.3 and 4,9.2 and clang 3.6.0)
- Boost [3] (tested with boost 1.55 and higher)
- Eigen [4] (>=3.2)
Requirements for the documentation :
------------------------------------
- Doxygen[5]
The tests require Catch[6] but it is downloaded automatically by Cmake in the project directory if needed.
Configuration Options :
=======================
These options are used by CMake to configure the project
- SPECMICP_NO_DEBUG
- bool (default OFF)
- if true, remove assert used in specmicp
- SPECMICP_USE_OPENMP :
- bool (default ON)
- use OpenMP to parallelize code
- SPECMICP_DEBUG_EQUATION_FD_JACOBIAN
- bool (default OFF)
- use a finite difference jacobian in specmicp
- - PYTHON_VERSION_3
- - bool (default ON)
- - if ON, compile cython module for python 3
-
- SPECMICP_BUILD_STATIC
- bool (default OFF)
- if ON, also build static libraries
- SPECMICP_BUILD_EXAMPLE
- bool (default ON)
- if ON, build the examples
- - SPECMICP_BUILD_CYTHON
- -bool (default ON)
- - if ON, build the cython/python module
Examples of configuration :
mkdir build; cd build
cmake .. -DSPECMICP_USE_OPENMP=ON -DCMAKE_C_COMPILER=[C compiler] -DCMAKE_CXX_COMPILER=[C++11 compiler] -DCMAKE_BUILD_TYPE=Release
Other example :
to install specmicp in '/opt/local'
mkdir build
cd build
cmake .. -DSPECMICP_BUILD_EXAMPLE=ON -DPYTHON_VERSION_3=OFF -DSPECMICP_USE_OPENMP=ON -DCMAKE_INSTALL_PREFIX=/opt/local -DCMAKE_BUILD_TYPE=release
make && make doc_html
make install
For a custom version of eigen 3:
-DEIGEN3_INCLUDE_DIR=[eigen3 directory]
For a custom version of boost :
-DBoost_NO_BOOST_CMAKE=true -DBOOSTROOT=[boost directory]
Tests
=====
The tests can be executed with through the ctest command
ctest [--output-on-failure]
ctest is part of the cmake framework.
+The commands `make check` and `make test` will also work.
[1]: http://www.cmake.org/
[2]: http://www.cmake.org/cmake/help/v3.0/
[3]: http://www.boost.org/
[4]: http://eigen.tuxfamily.org/
[5]: http://www.stack.nl/~dimitri/doxygen/
[6]: https://github.com/philsquared/Catch
diff --git a/README.md b/README.md
index 3e0e258..61d8702 100644
--- a/README.md
+++ b/README.md
@@ -1,107 +1,113 @@
SpecMiCP / ReactMiCP
====================
Overview
--------
SpecMiCP is a speciation solver to find the equilibrium state of a chemical
system. The system is based on a mixed complementarity formulation of the
equilibrium condition for minerals.
For a mineral with volume fraction Sm, the equilibrium condition is :
Sm >= 0, -log(IAPm/K) >= 0, -Sm*log(IAPm/K) = 0
where IAPm is the ion activity product and K the equilibrium constant.
This condition is reformulated using the penalized Fischer-Burmeister C-function and the system is solved
using a semismooth method.
ReactMiCP is a reactive transport solver built on top of specmicp.
It uses the operator splitting approach to couple transport and chemistry.
Modules
-------
SpecMiCP is not (yet) a program but a set of libraries that can be used to solve
specific problems.
The following modules are already available :
- **specmicp** : *core* of the library, set the system, and solve it
- **reactmicp** : the reactive transport solver
- **database** : manage the database, parse it from a file, swap the basis,
select the correct species, ...
- **micpsolver** : Solve a Mixed Complementarity problem
- **odeint** : integration methods for solving ordinary differential
equations (for problem involving kinetics for example)
- **dfpm** : a finite element module
-- **specmicp-cython** : a python interface to the SpecMiCP API
The **micpsolver** and **odeint** modules can be use independantly.
Examples of use are provided in the examples directory.
Using SpecMiCP
==============
Examples
--------
To build and install SpecMiCP/ReactMiCP see the INSTALL file.
To learn how to use the API the best is to look at the examples.
The starting point should be the leaching in CO2-saturated examples :
examples/reactmicp/saturated_react/carbonation.cpp.
This file is heavily commented.
Example of use of the Python interface can be found in the tests/cython directory.
Use in your own project
-----------------------
A cmake module can be used to find SpecMiCP in your own project. It will be installed at
<prefix>/share/specmicp/cmake/FindSpecMiCP.cmake
The python module can be used directly if it is in your python path.
Documentation
-------------
The API is documented with Doxygen and the documentation can be generated with the command :
make doc
A (maybe outdated) version of the doc can be found [here][3].
Warning
-------
The code is in development and the API is not considered stable yet.
+Python binding
+--------------
+
+A python binding is available at the following address :
+
+https://bitbucket.org/specmicp/specmicppy
+
About
=====
SpecMiCP is developped by F. Georget (fabieng aT princeton DoT edu). It is part
of my Ph.D. work. The purpose of the PhD is to develop a reactive transport model
to model the coupling between hydration, drying and carbonation in cement paste.
This Ph.D. is funded by [Princeton university][6], [Lafarge][4] and the [CSTB][5].
References :
- F. Georget, J. H. Prévost, and R. J. Vanderbei. A speciation solver for cement paste modeling and the semismooth Newton method . Cement and Concrete Research, 68(0):139--147, 2015.
- F. Georget, J. H. Prévost and B. Huet Validation of a reactive transport solver based on a semismooth speciation solver (submitted to Computational Geosciences)
A list of the references used in the code can be found in the [documentation][7].
[2]: http://www.empa.ch/plugin/template/empa/*/62204/---/l=1
[3]: http://www.princeton.edu/~fabieng/specmicpdoc/index.html
[4]: http://www.lafarge.com/en
[5]: http://www.cstb.fr/
[6]: http://princeton.edu
[7]: http://www.princeton.edu/~fabieng/specmicpdoc/citelist.html
diff --git a/cmake/FindCython.cmake b/cmake/FindCython.cmake
deleted file mode 100644
index 04aed1f..0000000
--- a/cmake/FindCython.cmake
+++ /dev/null
@@ -1,44 +0,0 @@
-# Find the Cython compiler.
-#
-# This code sets the following variables:
-#
-# CYTHON_EXECUTABLE
-#
-# See also UseCython.cmake
-
-#=============================================================================
-# Copyright 2011 Kitware, Inc.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#=============================================================================
-
-# Use the Cython executable that lives next to the Python executable
-# if it is a local installation.
-find_package( PythonInterp )
-if( PYTHONINTERP_FOUND )
- get_filename_component( _python_path ${PYTHON_EXECUTABLE} PATH )
- find_program( CYTHON_EXECUTABLE
- NAMES cython cython.bat cython3
- HINTS ${_python_path}
- )
-else()
- find_program( CYTHON_EXECUTABLE
- NAMES cython cython.bat cython3
- )
-endif()
-
-
-include( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS( Cython REQUIRED_VARS CYTHON_EXECUTABLE )
-
-mark_as_advanced( CYTHON_EXECUTABLE )
diff --git a/cmake/UseCython.cmake b/cmake/UseCython.cmake
deleted file mode 100644
index 86aa7d8..0000000
--- a/cmake/UseCython.cmake
+++ /dev/null
@@ -1,295 +0,0 @@
-# Define a function to create Cython modules.
-#
-# For more information on the Cython project, see http://cython.org/.
-# "Cython is a language that makes writing C extensions for the Python language
-# as easy as Python itself."
-#
-# This file defines a CMake function to build a Cython Python module.
-# To use it, first include this file.
-#
-# include( UseCython )
-#
-# Then call cython_add_module to create a module.
-#
-# cython_add_module( <module_name> <src1> <src2> ... <srcN> )
-#
-# To create a standalone executable, the function
-#
-# cython_add_standalone_executable( <executable_name> [MAIN_MODULE src1] <src1> <src2> ... <srcN> )
-#
-# To avoid dependence on Python, set the PYTHON_LIBRARY cache variable to point
-# to a static library. If a MAIN_MODULE source is specified,
-# the "if __name__ == '__main__':" from that module is used as the C main() method
-# for the executable. If MAIN_MODULE, the source with the same basename as
-# <executable_name> is assumed to be the MAIN_MODULE.
-#
-# Where <module_name> is the name of the resulting Python module and
-# <src1> <src2> ... are source files to be compiled into the module, e.g. *.pyx,
-# *.py, *.c, *.cxx, etc. A CMake target is created with name <module_name>. This can
-# be used for target_link_libraries(), etc.
-#
-# The sample paths set with the CMake include_directories() command will be used
-# for include directories to search for *.pxd when running the Cython complire.
-#
-# Cache variables that effect the behavior include:
-#
-# CYTHON_ANNOTATE
-# CYTHON_NO_DOCSTRINGS
-# CYTHON_FLAGS
-#
-# Source file properties that effect the build process are
-#
-# CYTHON_IS_CXX
-#
-# If this is set of a *.pyx file with CMake set_source_files_properties()
-# command, the file will be compiled as a C++ file.
-#
-# See also FindCython.cmake
-
-#=============================================================================
-# Copyright 2011 Kitware, Inc.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#=============================================================================
-
-# Configuration options.
-set( CYTHON_ANNOTATE OFF
- CACHE BOOL "Create an annotated .html file when compiling *.pyx." )
-set( CYTHON_NO_DOCSTRINGS OFF
- CACHE BOOL "Strip docstrings from the compiled module." )
-set( CYTHON_FLAGS "" CACHE STRING
- "Extra flags to the cython compiler." )
-mark_as_advanced( CYTHON_ANNOTATE CYTHON_NO_DOCSTRINGS CYTHON_FLAGS )
-
-find_package( Cython REQUIRED )
-find_package( PythonLibs REQUIRED )
-
-set( CYTHON_CXX_EXTENSION "cxx" )
-set( CYTHON_C_EXTENSION "c" )
-
-# Create a *.c or *.cxx file from a *.pyx file.
-# Input the generated file basename. The generate file will put into the variable
-# placed in the "generated_file" argument. Finally all the *.py and *.pyx files.
-function( compile_pyx _name generated_file )
- # Default to assuming all files are C.
- set( cxx_arg "" )
- set( extension ${CYTHON_C_EXTENSION} )
- set( pyx_lang "C" )
- set( comment "Compiling Cython C source for ${_name}..." )
-
- set( cython_include_directories "" )
- set( pxd_dependencies "" )
- set( c_header_dependencies "" )
- set( pyx_locations "" )
-
- foreach( pyx_file ${ARGN} )
- get_filename_component( pyx_file_basename "${pyx_file}" NAME_WE )
-
- # Determine if it is a C or C++ file.
- get_source_file_property( property_is_cxx ${pyx_file} CYTHON_IS_CXX )
- if( ${property_is_cxx} )
- set( cxx_arg "--cplus" )
- set( extension ${CYTHON_CXX_EXTENSION} )
- set( pyx_lang "CXX" )
- set( comment "Compiling Cython CXX source for ${_name}..." )
- endif()
-
- # Get the include directories.
- get_source_file_property( pyx_location ${pyx_file} LOCATION )
- get_filename_component( pyx_path ${pyx_location} PATH )
- get_directory_property( cmake_include_directories DIRECTORY ${pyx_path} INCLUDE_DIRECTORIES )
- list( APPEND cython_include_directories ${cmake_include_directories} )
- list( APPEND pyx_locations "${pyx_location}" )
-
- # Determine dependencies.
- # Add the pxd file will the same name as the given pyx file.
- unset( corresponding_pxd_file CACHE )
- find_file( corresponding_pxd_file ${pyx_file_basename}.pxd
- PATHS "${pyx_path}" ${cmake_include_directories}
- NO_DEFAULT_PATH )
- if( corresponding_pxd_file )
- list( APPEND pxd_dependencies "${corresponding_pxd_file}" )
- endif()
-
- # pxd files to check for additional dependencies.
- set( pxds_to_check "${pyx_file}" "${pxd_dependencies}" )
- set( pxds_checked "" )
- set( number_pxds_to_check 1 )
- while( ${number_pxds_to_check} GREATER 0 )
- foreach( pxd ${pxds_to_check} )
- list( APPEND pxds_checked "${pxd}" )
- list( REMOVE_ITEM pxds_to_check "${pxd}" )
-
- # check for C header dependencies
- file( STRINGS "${pxd}" extern_from_statements
- REGEX "cdef[ ]+extern[ ]+from.*$" )
- foreach( statement ${extern_from_statements} )
- # Had trouble getting the quote in the regex
- string( REGEX REPLACE "cdef[ ]+extern[ ]+from[ ]+[\"]([^\"]+)[\"].*" "\\1" header "${statement}" )
- unset( header_location CACHE )
- find_file( header_location ${header} PATHS ${cmake_include_directories} )
- if( header_location )
- list( FIND c_header_dependencies "${header_location}" header_idx )
- if( ${header_idx} LESS 0 )
- list( APPEND c_header_dependencies "${header_location}" )
- endif()
- endif()
- endforeach()
-
- # check for pxd dependencies
-
- # Look for cimport statements.
- set( module_dependencies "" )
- file( STRINGS "${pxd}" cimport_statements REGEX cimport )
- foreach( statement ${cimport_statements} )
- if( ${statement} MATCHES from )
- string( REGEX REPLACE "from[ ]+([^ ]+).*" "\\1" module "${statement}" )
- else()
- string( REGEX REPLACE "cimport[ ]+([^ ]+).*" "\\1" module "${statement}" )
- endif()
- list( APPEND module_dependencies ${module} )
- endforeach()
- list( REMOVE_DUPLICATES module_dependencies )
- # Add the module to the files to check, if appropriate.
- foreach( module ${module_dependencies} )
- unset( pxd_location CACHE )
- find_file( pxd_location ${module}.pxd
- PATHS "${pyx_path}" ${cmake_include_directories} NO_DEFAULT_PATH )
- if( pxd_location )
- list( FIND pxds_checked ${pxd_location} pxd_idx )
- if( ${pxd_idx} LESS 0 )
- list( FIND pxds_to_check ${pxd_location} pxd_idx )
- if( ${pxd_idx} LESS 0 )
- list( APPEND pxds_to_check ${pxd_location} )
- list( APPEND pxd_dependencies ${pxd_location} )
- endif() # if it is not already going to be checked
- endif() # if it has not already been checked
- endif() # if pxd file can be found
- endforeach() # for each module dependency discovered
- endforeach() # for each pxd file to check
- list( LENGTH pxds_to_check number_pxds_to_check )
- endwhile()
- endforeach() # pyx_file
-
- # Set additional flags.
- if( CYTHON_ANNOTATE )
- set( annotate_arg "--annotate" )
- endif()
-
- if( CYTHON_NO_DOCSTRINGS )
- set( no_docstrings_arg "--no-docstrings" )
- endif()
-
- if( "${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR
- "${CMAKE_BUILD_TYPE}" STREQUAL "RelWithDebInfo" )
- set( cython_debug_arg "--gdb" )
- endif()
-
- if( "${PYTHONLIBS_VERSION_STRING}" MATCHES "^2." )
- set( version_arg "-2" )
- elseif( "${PYTHONLIBS_VERSION_STRING}" MATCHES "^3." )
- set( version_arg "-3" )
- else()
- set( version_arg )
- endif()
-
- # Include directory arguments.
- list( REMOVE_DUPLICATES cython_include_directories )
- set( include_directory_arg "" )
- foreach( _include_dir ${cython_include_directories} )
- set( include_directory_arg ${include_directory_arg} "-I" "${_include_dir}" )
- endforeach()
-
- # Determining generated file name.
- set( _generated_file "${CMAKE_CURRENT_BINARY_DIR}/${_name}.${extension}" )
- set_source_files_properties( ${_generated_file} PROPERTIES GENERATED TRUE )
- set( ${generated_file} ${_generated_file} PARENT_SCOPE )
-
- list( REMOVE_DUPLICATES pxd_dependencies )
- list( REMOVE_DUPLICATES c_header_dependencies )
-
- # Add the command to run the compiler.
- add_custom_command( OUTPUT ${_generated_file}
- COMMAND ${CYTHON_EXECUTABLE}
- ARGS ${cxx_arg} ${include_directory_arg} ${version_arg}
- ${annotate_arg} ${no_docstrings_arg} ${cython_debug_arg} ${CYTHON_FLAGS}
- --output-file ${_generated_file} ${pyx_locations}
- DEPENDS ${pyx_locations} ${pxd_dependencies}
- IMPLICIT_DEPENDS ${pyx_lang} ${c_header_dependencies}
- COMMENT ${comment}
- )
-
- # Remove their visibility to the user.
- set( corresponding_pxd_file "" CACHE INTERNAL "" )
- set( header_location "" CACHE INTERNAL "" )
- set( pxd_location "" CACHE INTERNAL "" )
-endfunction()
-
-# cython_add_module( <name> src1 src2 ... srcN )
-# Build the Cython Python module.
-function( cython_add_module _name )
- set( pyx_module_sources "" )
- set( other_module_sources "" )
- foreach( _file ${ARGN} )
- if( ${_file} MATCHES ".*\\.py[x]?$" )
- list( APPEND pyx_module_sources ${_file} )
- else()
- list( APPEND other_module_sources ${_file} )
- endif()
- endforeach()
- compile_pyx( ${_name} generated_file ${pyx_module_sources} )
- include_directories( ${PYTHON_INCLUDE_DIRS} )
- python_add_module( ${_name} ${generated_file} ${other_module_sources} )
- if( APPLE )
- set_target_properties( ${_name} PROPERTIES LINK_FLAGS "-undefined dynamic_lookup" )
- else()
- target_link_libraries( ${_name} ${PYTHON_LIBRARIES} )
- endif()
-endfunction()
-
-include( CMakeParseArguments )
-# cython_add_standalone_executable( _name [MAIN_MODULE src3.py] src1 src2 ... srcN )
-# Creates a standalone executable the given sources.
-function( cython_add_standalone_executable _name )
- set( pyx_module_sources "" )
- set( other_module_sources "" )
- set( main_module "" )
- cmake_parse_arguments( cython_arguments "" "MAIN_MODULE" "" ${ARGN} )
- include_directories( ${PYTHON_INCLUDE_DIRS} )
- foreach( _file ${cython_arguments_UNPARSED_ARGUMENTS} )
- if( ${_file} MATCHES ".*\\.py[x]?$" )
- get_filename_component( _file_we ${_file} NAME_WE )
- if( "${_file_we}" STREQUAL "${_name}" )
- set( main_module "${_file}" )
- elseif( NOT "${_file}" STREQUAL "${cython_arguments_MAIN_MODULE}" )
- set( PYTHON_MODULE_${_file_we}_static_BUILD_SHARED OFF )
- compile_pyx( "${_file_we}_static" generated_file "${_file}" )
- list( APPEND pyx_module_sources "${generated_file}" )
- endif()
- else()
- list( APPEND other_module_sources ${_file} )
- endif()
- endforeach()
-
- if( cython_arguments_MAIN_MODULE )
- set( main_module ${cython_arguments_MAIN_MODULE} )
- endif()
- if( NOT main_module )
- message( FATAL_ERROR "main module not found." )
- endif()
- get_filename_component( main_module_we "${main_module}" NAME_WE )
- set( CYTHON_FLAGS ${CYTHON_FLAGS} --embed )
- compile_pyx( "${main_module_we}_static" generated_file ${main_module} )
- add_executable( ${_name} ${generated_file} ${pyx_module_sources} ${other_module_sources} )
- target_link_libraries( ${_name} ${PYTHON_LIBRARIES} ${pyx_module_libs} )
-endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
deleted file mode 100644
index 0c83da1..0000000
--- a/cython/CMakeLists.txt
+++ /dev/null
@@ -1,91 +0,0 @@
-# ======================= #
-# #
-# Python specmicp lib #
-# #
-# ======================= #
-
-# Build the cython interface
-# ==========================
-
-# Import the correct version of python
-
-option(PYTHON_VERSION_3 "Version of python for cython compilation" ON)
-
-if (PYTHON_VERSION_3)
- find_package(PythonInterp 3 REQUIRED)
- find_package(PythonLibs 3 REQUIRED)
-else()
- find_package(PythonInterp 2.7 REQUIRED)
- find_package(PythonLibs 2.7 REQUIRED)
-endif()
-
-include_directories(${PYTHON_INCLUDE_PATH})
-
-# include cython only once python is configured
-include(UseCython)
-
-# main variables
-# ===============
-
-# directories
-# -----------
-set(PY_SPECMICP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/specmicp)
-set(PY_SPECMICP_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/specmicp)
-set(PY_INCLUDES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/includes)
-
-
-# common includes
-# ===============
-
-add_custom_target(cython_includes SOURCES
- ${PY_INCLUDES_DIR}/memory.pxd
- ${PY_INCLUDES_DIR}/eigen_set.hpp
- ${PY_INCLUDES_DIR}/eigen.pxd
-)
-
-# SpecMiCP module
-# ===============
-add_subdirectory(specmicp)
-
-
-# setup.py
-set(CYTHON_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR})
-configure_file(setup.py.in ${CYTHON_BINARY_DIR}/setup.py @ONLY)
-configure_file(install_python.cmake.in ${CYTHON_BINARY_DIR}/install_python.cmake @ONLY)
-install(SCRIPT "${CYTHON_BINARY_DIR}/install_python.cmake")
-
-# ========== #
-# #
-# TEST #
-# #
-# ========== #
-
-# Prelude
-# =======
-
-# directories
-# -----------
-set(TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tests/cython)
-set(BINARY_TEST_DIR ${PROJECT_BINARY_DIR}/tests)
-
-# variables to configure the scripts
-# ----------------------------------
-set(python_module_path ${CMAKE_CURRENT_BINARY_DIR})
-set(database_path ${CMAKE_CURRENT_BINARY_DIR}/../data/cemdata_specmicp.js)
-
-# macro to configure the scripts
-# -------------------------------
-macro(configure_python_test test_name)
-configure_file(${TEST_DIR}/${test_name} ${BINARY_TEST_DIR}${CMAKE_FILES_DIRECTORY}/${test_name} @ONLY)
-file(COPY ${BINARY_TEST_DIR}${CMAKE_FILES_DIRECTORY}/${test_name}
- DESTINATION ${BINARY_TEST_DIR}
- FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ
- GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
-endmacro(configure_python_test)
-
-# Scripts
-# =======
-# database unittest
-configure_python_test(database.py)
-# test specmicp
-configure_python_test(test_specmicp.py)
diff --git a/cython/includes/eigen.pxd b/cython/includes/eigen.pxd
deleted file mode 100644
index 9281328..0000000
--- a/cython/includes/eigen.pxd
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton University
-# All rights reserved.
-
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-# notice, this list of conditions and the following disclaimer in the
-# documentation and/or other materials provided with the distribution.
-# * Neither the name of SpecMiCP nor the
-# names of its contributors may be used to endorse or promote products
-# derived from this software without specific prior written permission.
-
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-# Includes from Eigen
-#
-# This is kept simple on purpose
-cdef extern from "<Eigen/Dense>" namespace "Eigen":
- cdef cppclass Matrix[T, U, V]:
- Matrix()
- T& operator()(int, int)
- T& operator()(int)
-
- # A matrix
- cdef cppclass MatrixXd:
- MatrixXd()
- MatrixXd(int, int)
- MatrixXd(const MatrixXd& other)
- void setZero()
- void setZero(int, int)
- float& operator()(int, int) # read access
-
- # a vector
- cdef cppclass VectorXd:
- VectorXd()
- VectorXd(int)
- VectorXd(const VectorXd& other)
- void setZero()
- void setZero(int)
-
- float& operator()(int) # read access
-
-# write
-cdef extern from "eigen_set.hpp":
- cdef void vector_setitem(VectorXd&, int row, float value)
- cdef void vector_additem(VectorXd&, int row, float value)
- cdef void matrix_setitem(MatrixXd&, int row, int col, float value)
- cdef void matrix_additem(MatrixXd&, int row, int col, float value)
diff --git a/cython/includes/eigen_set.hpp b/cython/includes/eigen_set.hpp
deleted file mode 100644
index 2b5bda1..0000000
--- a/cython/includes/eigen_set.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*-------------------------------------------------------
-
-Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton University
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- * Neither the name of the Princeton University nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
----------------------------------------------------------*/
-
-#ifndef SPECMICP_CYTHON_EIGEN
-#define SPECMICP_CYTHON_EIGEN
-
-#include <Eigen/Core>
-
-// Cython do not accept left-value references
-// this is a workaround to set an value in a vector or a matrix
-
-inline void vector_setitem(Eigen::VectorXd& vec, int row, double value) {
- vec(row) = value;
-}
-
-inline void vector_additem(Eigen::VectorXd& vec, int row, double value) {
- vec(row) += value;
-}
-
-
-inline void matrix_setitem(Eigen::MatrixXd& mat, int row, int col, double value) {
- mat(row, col) = value;
-}
-
-inline void matrix_additem(Eigen::MatrixXd& mat, int row, int col, double value) {
- mat(row, col) += value;
-}
-
-#endif // SPECMICP_CYTHON_EIGEN
-
diff --git a/cython/includes/memory.pxd b/cython/includes/memory.pxd
deleted file mode 100644
index f1f3575..0000000
--- a/cython/includes/memory.pxd
+++ /dev/null
@@ -1,14 +0,0 @@
-# definition from <memory>
-#
-cdef extern from "<memory>" namespace "std":
- #
- # The shared ptr
- # note : there is no overloading of operator->
- # the true object is accessed through the get() member function
- #
- cdef cppclass shared_ptr[T]:
- shared_ptr()
- shared_ptr(shared_ptr[T])
- T* get()
-
- shared_ptr[T] make_shared[T]()
diff --git a/cython/install_python.cmake.in b/cython/install_python.cmake.in
deleted file mode 100644
index baf2c6e..0000000
--- a/cython/install_python.cmake.in
+++ /dev/null
@@ -1,9 +0,0 @@
-execute_process(COMMAND @PYTHON_EXECUTABLE@ setup.py install --prefix @CMAKE_INSTALL_PREFIX@
- RESULT_VARIABLE retcode
- ERROR_VARIABLE error_setup_py
- OUTPUT_VARIABLE output_setup_py
- WORKING_DIRECTORY @CYTHON_BINARY_DIR@
- )
-message(STATUS ${retcode})
-message(STATUS ${output_setup_py})
-message(STATUS ${error_setup_py})
diff --git a/cython/setup.py.in b/cython/setup.py.in
deleted file mode 100644
index 6226bef..0000000
--- a/cython/setup.py.in
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-
-setup(name='specmicp',
- version='@SPECMICP_VERSION@',
- description='Python interface for SpecMiCP ',
- author='Fabien Georget',
- author_email='fabieng@princeton.edu',
- url='https://bitbucket.org/specmicp/specmicp',
- packages=['specmicp'],
- package_dir={'specmicp': 'specmicp'},
- package_data={'specmicp': ['*.so']}
- )
\ No newline at end of file
diff --git a/cython/specmicp/CMakeLists.txt b/cython/specmicp/CMakeLists.txt
deleted file mode 100644
index 6160f68..0000000
--- a/cython/specmicp/CMakeLists.txt
+++ /dev/null
@@ -1,123 +0,0 @@
-# Build the python module : SpecMiCP
-# ==================================
-
-set(PY_INCLUDES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../includes)
-
-include_directories(${PY_INCLUDES_DIR})
-include_directories(${EIGEN3_INCLUDE_DIR})
-include_directories(${PROJECT_SOURCE_DIR})
-include_directories(${JSONCPP_DIR})
-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-
-set(cython_specmicp_files
- __init__.py
- database.pxd
- database.pyx
- solution.pxd
- solution.pyx
- constraints.pxd
- constraints.pyx
- solver.pxd
- solver.pyx
- is_solver_successful.hpp
- set_units.hpp
- init_log.hpp
- logger.pxd
- logger.pyx
- cement_hydration.py
-
- units.pxd
- solver_options.pxd
-
-)
-
-
-#add_library(specmicp_cython_database SHARED ${DATABASE_LIBFILE})
-#add_library(specmicp_cython_specmicp SHARED ${SPECMICP_LIBFILE})
-
-# database
-# ---------
-
-
-set_source_files_properties(
- database.pyx
- PROPERTIES CYTHON_IS_CXX TRUE )
-
-cython_add_module(database database.pyx)
-target_link_libraries(database specmicp_database specmicp)
-
-# solution
-# --------
-
-set_source_files_properties(
- solution.pyx
- PROPERTIES CYTHON_IS_CXX TRUE )
-
-cython_add_module(solution solution.pyx)
-target_link_libraries(solution specmicp_database specmicp)
-
-# constraints
-# -----------
-set_source_files_properties(
- constraints.pyx
- PROPERTIES CYTHON_IS_CXX TRUE )
-
-cython_add_module(constraints constraints.pyx)
-target_link_libraries(constraints specmicp_database specmicp)
-
-# solver
-# -----
-
-set_source_files_properties(
- solver.pyx
- PROPERTIES CYTHON_IS_CXX TRUE
-)
-
-cython_add_module(solver solver.pyx)
-target_link_libraries(solver specmicp_database specmicp)
-
-
-# logger
-# -----
-
-set_source_files_properties(
- logger.pyx
- PROPERTIES CYTHON_IS_CXX TRUE
-)
-
-cython_add_module(logger logger.pyx)
-
-
-
-# specmicp module
-# ---------------
-
-set(PURE_PYTHON_FILES
- __init__.py
- cement_hydration.py
-)
-
-add_custom_target(cython_specmicp ALL
- DEPENDS database solution constraints solver logger ${PURE_PYTHON_FILES}
- COMMENT "Built the python specmicp module"
- SOURCES ${cython_specmicp_files}
-)
-
-
-macro(COPY_PURE_PYTHON_FILE in_file out_file target)
- if(${in_file} IS_NEWER_THAN ${out_file})
- add_custom_command (
- TARGET ${target}
- COMMAND ${CMAKE_COMMAND}
- ARGS -E copy ${in_file} ${out_file}
- )
- endif()
-endmacro(COPY_PURE_PYTHON_FILE)
-
-
-
-foreach(in_file ${PURE_PYTHON_FILES})
- COPY_PURE_PYTHON_FILE(${CMAKE_CURRENT_SOURCE_DIR}/${in_file} ${CMAKE_CURRENT_BINARY_DIR}/${in_file} cython_specmicp)
-endforeach()
-
-
diff --git a/cython/specmicp/__init__.py b/cython/specmicp/__init__.py
deleted file mode 100644
index 1cb6f47..0000000
--- a/cython/specmicp/__init__.py
+++ /dev/null
@@ -1,28 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/cython/specmicp/cement_hydration.py b/cython/specmicp/cement_hydration.py
deleted file mode 100644
index c73a333..0000000
--- a/cython/specmicp/cement_hydration.py
+++ /dev/null
@@ -1,281 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-import specmicp.database as database
-import specmicp.constraints as formulation
-import specmicp.solver
-
-MASS_PERCENT_INDEX = 0
-HYDRATION_INDEX = 1
-
-
-def hydration(
- minerals,
- wc,
- database_path="",
- database_manager=None,
- aqueous_species=None,
- percent_v_entrained_air=0.0,
- list_minerals_to_keep=None,
- list_extra_component=[],
- length_unit="meter",
- previous_sol=None,
- saturated_system=False
- ):
- """Thermodynamic Cement hydration
-
- Return a SpecMiCPSolution
- The first argument is a dictionary :
- {label: (mass_percent, hydration degree)}
-
- A new database is created for each p
-
- Example :
- >>> sol = hydration(
- {"C3S": (0.8, 1.0), "C3A": (0.1, 1.0), "C4AF": (0.1, 1.0)},
- 0.4,
- "../data/cemdata.js",
- percent_v_entrained_air=0.0)
-
- """
- if database_manager is None:
- db = database.DatabaseManager(database_path)
- swapping = {
- "H[+]": "HO[-]",
- "Al[3+]": "Al(OH)4[-]",
- "Fe[2+]": "Fe(OH)4[-]",
- "Si(OH)4": "SiO(OH)3[-]"
- }
- db.swap_components(swapping)
- db.remove_gas_phases()
- else:
- db = database_manager
-
-
- if length_unit == "meter":
- scaling = 1.0
- elif length_unit == "decimeter":
- scaling = 1e3
- elif length_unit == "centimer":
- scaling = 1e6
- else:
- raise ValueError("Unknown length unit")
-
- scaling_M = 1.0
-
- rho_minerals = []
- is_kinetic = []
-
- # find the cement mass
- # --------------------
- sum_for_cement_mass = 0.0
-
- for (label, value) in minerals.items():
- try:
- idm = db.mineral_label_to_id(label)
- rho_minerals.append(scaling_M/scaling*db.density_mineral(idm))
- is_kinetic.append(False)
- except ValueError:
- idm = db.mineral_kinetic_label_to_id(label)
- rho_minerals.append(scaling_M/scaling*db.density_mineral_kinetic(idm))
- is_kinetic.append(True)
- sum_for_cement_mass += value[MASS_PERCENT_INDEX] / rho_minerals[-1]
-
- sum_for_cement_mass += wc / (997.0 / scaling)
-
- mc = (1.0 - percent_v_entrained_air) / sum_for_cement_mass
- inert_volume = 0.0
-
- # set the formulation
- # -------------------
- system = formulation.SpecMiCPFormulation(db)
-
- for (index, (label, value)) in enumerate(minerals.items()):
- reactant_mass = value[MASS_PERCENT_INDEX] * mc
- concentration = value[HYDRATION_INDEX] * reactant_mass
- inert = (1.0 - value[HYDRATION_INDEX]) * reactant_mass
- if is_kinetic[index]:
- concentration /= scaling_M*db.molar_mass_mineral_kinetic(idm)
- inert /= rho_minerals[index]
- else:
- concentration /= scaling_M*db.molar_mass_mineral(idm)
- inert /= rho_minerals[index]
- system.add_mineral(label, concentration)
- inert_volume += inert
-
- system.set_inert_volume_fraction(inert_volume)
- system.set_mass_solution(wc * mc)
-
- if aqueous_species is not None:
- for (label, value) in aqueous_species.items():
- system.add_aqueous_species(label, value)
-
- if list_minerals_to_keep is not None:
- system.set_list_minerals(list_minerals_to_keep)
-
- system.initialize_system()
- if saturated_system:
- system.set_saturated_system()
- system.set_charge_keeper("HO[-]")
-
-
- # solve the problem
- # -----------------
- the_solver = specmicp.solver.SpecMiCPSolver(db, system, previous_sol)
- the_solver.set_length_unit(length_unit)
- the_solver.set_maximum_step_length(20, 100)
- the_solver.enable_non_monotone_linesearch()
- the_solver.disable_condition_check()
- the_solver.set_tolerances(1e-8, 1e-12)
- the_solver.set_non_ideality_tolerance(1e-12)
- if previous_sol is None:
- map_init = {"HO[-]": -2.0, "Ca[2+]": -2.0, "SiO(OH)3[-]": -5.0}
- extra_components = {"Al(OH)4[-]": -3.0, "SO4[2-]": -3.0, "Fe(OH)4[-]": -4.0}
- for (label, value) in extra_components.items():
- try:
- _ = db.component_label_to_id(label)
- map_init[label] = value
- except ValueError:
- pass
- the_solver.initialize_variables(0.5, map_init)
- the_solver.solve()
-
- # return the solution
- # -------------------
- return the_solver.get_solution()
-
-
-def hydration_oxyde(
- oxyde_formulation,
- density_cement,
- wc,
- loss_of_ignition,
- database_path="",
- database_manager=None,
- aqueous_species=None,
- percent_v_entrained_air=0.0,
- list_minerals_to_keep=None,
- list_extra_component=[],
- length_unit="meter",
- previous_sol=None,
- saturated_system=False,
- degree_hydration=1.0
- ):
- """Thermodynamic Cement hydration
-
- No hydration degree
-
- Return a SpecMiCPSolution
- The first argument is a dictionary :
- {label: (mass_percent, hydration degree)}
-
- A new database is created for each p
-
- """
- if database_manager is None:
- db = database.DatabaseManager(database_path)
- swapping = {
- "H[+]": "HO[-]",
- "Al[3+]": "Al(OH)4[-]",
- "Fe[2+]": "Fe(OH)4[-]",
- "Si(OH)4": "SiO(OH)3[-]"
- }
- db.swap_components(swapping)
- db.remove_gas_phases()
- else:
- db = database_manager
-
-
- if length_unit == "meter":
- scaling = 1.0
- elif length_unit == "decimeter":
- scaling = 1e3
- elif length_unit == "centimer":
- scaling = 1e6
- else:
- raise ValueError("Unknown length unit")
-
- scaling_M = 1.0
-
-
- # find the cement mass
- # --------------------
-
- sum_for_cement_mass = 1.0/density_cement + wc / (997.0 / scaling)
-
- mc = (1.0 - percent_v_entrained_air) / sum_for_cement_mass
-
- # set the formulation
- # -------------------
- system = formulation.SpecMiCPFormulation(db)
-
- for (index, (label, value)) in enumerate(oxyde_formulation.items()):
- concentration = value * mc * degree_hydration
- concentration /= scaling_M*db.l_molar_mass_mineral_kinetic(label)
- system.add_mineral(label, concentration)
- system.set_inert_volume_fraction(mc*(1.0-degree_hydration)/density_cement)
- system.set_mass_solution(wc * mc + loss_of_ignition * mc)
-
- if aqueous_species is not None:
- for (label, value) in aqueous_species.items():
- system.add_aqueous_species(label, value)
-
- if list_minerals_to_keep is not None:
- system.set_list_minerals(list_minerals_to_keep)
-
- system.initialize_system()
- if saturated_system:
- system.set_saturated_system()
- system.set_charge_keeper("HO[-]")
-
-
- # solve the problem
- # -----------------
- the_solver = specmicp.solver.SpecMiCPSolver(db, system, previous_sol)
- the_solver.set_length_unit(length_unit)
- the_solver.set_maximum_step_length(20, 100)
- the_solver.enable_non_monotone_linesearch()
- the_solver.disable_condition_check()
- the_solver.set_tolerances(1e-8, 1e-12)
- the_solver.set_non_ideality_tolerance(1e-12)
- if previous_sol is None:
- map_init = {"HO[-]": -2.0, "Ca[2+]": -2.0, "SiO(OH)3[-]": -5.0}
- extra_components = {"Al(OH)4[-]": -3.0, "SO4[2-]": -3.0, "Fe(OH)4[-]": -4.0}
- for (label, value) in extra_components.items():
- try:
- _ = db.component_label_to_id(label)
- map_init[label] = value
- except ValueError:
- pass
- the_solver.initialize_variables(0.5, map_init)
- the_solver.solve()
-
- # return the solution
- # -------------------
- return the_solver.get_solution()
diff --git a/cython/specmicp/constraints.pxd b/cython/specmicp/constraints.pxd
deleted file mode 100644
index 2c45607..0000000
--- a/cython/specmicp/constraints.pxd
+++ /dev/null
@@ -1,92 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-from eigen cimport VectorXd
-from libcpp.map cimport map as cmap
-from libcpp.string cimport string
-from libcpp.vector cimport vector
-
-from memory cimport shared_ptr
-from database cimport DatabaseManager, DataContainer
-
-# The constraints
-# ---------------
-cdef extern from "specmicp/adimensional/adimensional_system_structs.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemConstraints:
- AdimensionalSystemConstraints()
- AdimensionalSystemConstraints(const AdimensionalSystemConstraints& other)
-
- VectorXd total_concentrations
-
- void set_total_concentrations(const VectorXd&)
-
- void enable_conservation_water()
- void disable_conservation_water()
- void set_saturated_system()
-
- void disable_surface_model()
- void enable_surface_model(double)
-
- void set_charge_keeper(int)
- void add_fixed_fugacity_gas(int, int, float)
- void add_fixed_activity_component(int, double)
-
- void set_inert_volume_fraction(double)
-
-# The formulation of the problem
-# ------------------------------
-cdef extern from "specmicp/problem_solver/formulation.hpp" namespace "specmicp":
- cdef cppclass Formulation:
- Formulation()
- void set_mass_solution(double)
- void add_aqueous_species(const string&, double) except +
- void add_mineral(const string&, double) except +
- void keep_component(const string&)
- void set_minerals_list(const vector[string]& list)
-
-# Dissolve the formulation
-# ------------------------
-cdef extern from "specmicp/problem_solver/dissolver.hpp" namespace "specmicp":
- cdef cppclass Dissolver:
- Dissolver(shared_ptr[DataContainer])
- VectorXd dissolve(const Formulation&) except +
- VectorXd get_total_concentration()
-
-# Wrapper for the constraints
-# ---------------------------
-cdef class SpecMiCPConstraints:
- cdef DatabaseManager database
- cdef AdimensionalSystemConstraints* constraints
- cdef AdimensionalSystemConstraints* _get(self)
-
-# Wrapper for the formulation
-# ---------------------------
-cdef class SpecMiCPFormulation(SpecMiCPConstraints):
- cdef Formulation* formulation
diff --git a/cython/specmicp/constraints.pyx b/cython/specmicp/constraints.pyx
deleted file mode 100644
index 8f702f9..0000000
--- a/cython/specmicp/constraints.pyx
+++ /dev/null
@@ -1,184 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-from database cimport DatabaseManager
-from constraints cimport SpecMiCPConstraints, AdimensionalSystemConstraints, SpecMiCPFormulation
-from eigen cimport VectorXd, vector_setitem, vector_additem
-from libcpp.utility cimport pair
-from cython.operator cimport dereference
-
-cdef class SpecMiCPConstraints:
- """A class managing the SpecMiCP constraints"""
-
- def __cinit__(self, DatabaseManager database not None):
- self.database = database
- self.constraints = new AdimensionalSystemConstraints()
- def __dealloc__(self):
- del self.constraints
- cdef AdimensionalSystemConstraints* _get(self):
- return self.constraints
-
- # Total concentrations
- # --------------------
-
- def set_total_concentrations(self, dictionary_total_concs):
- """Set the total concentrations
-
- dictionary_total_concs is a dictionary mapping the labels of components
- to their total concentrations.
- """
- cdef VectorXd total_concs
- cdef int index
- total_concs.setZero(self.database.nb_component)
- for (key, value) in dictionary_total_concs.items():
- index = self.database.component_label_to_id(key)
- vector_setitem(total_concs, index, value)
- self.constraints.set_total_concentrations(total_concs)
-
- def add_total_concentrations(self, dictionary_total_concs):
- """Set the total concentrations
-
- dictionary_total_concs is a dictionary mapping the labels of components
- to their total concentrations.
- """
- cdef int index
- for (key, value) in dictionary_total_concs.items():
- index = self.database.component_label_to_id(key)
- vector_additem(self.constraints.total_concentrations, index, value)
-
- def get_total_concentration(self, label):
- """Return the total concentration for "label" """
- index = self.database.component_label_to_id(label)
- return self.constraints.total_concentrations(index)
-
- # Water conservation
- # ------------------
-
- def enable_conservation_water(self):
- """Enable the conservation of water"""
- self.constraints.enable_conservation_water()
- def disable_conservation_water(self):
- """Disable the conservation of water.
-
- No equation is solved for the water component in this case."""
- self.constraints.disable_conservation_water()
- def set_saturated_system(self):
- """The system is saturated with water"""
- self.constraints.set_saturated_system()
-
- # Surface model
- # -------------
-
- def enable_surface_model(self, site_concentrations):
- """Enable the surface sorption model.
-
- The total concentration of sorption site is 'site_concentrations'"""
- self.constraints.enable_surface_model(site_concentrations)
- def disable_surface_model(self):
- """Disable the surface sorption model"""
- self.constraints.disable_surface_model()
-
- # components
- # ----------
-
- def set_charge_keeper(self, label):
- """Set the charge keeper to be 'label'
-
- The charge keeper is in charge of the electroneutrality equation"""
- cdef int index
- index = self.database.component_label_to_id(label)
- self.constraints.set_charge_keeper(index)
- def add_fixed_fugacity_gas(self, gas_label, component_label, log_fugacity):
- """Set 'gas_label' to be a fixed fugacity gas"""
- cdef int g_index, c_index
- g_index = self.database.gas_label_to_id(gas_label)
- c_index = self.database.component_label_to_id(component_label)
- self.constraints.add_fixed_fugacity_gas(g_index, c_index, log_fugacity)
- def add_fixed_activity_component(self, component_label, log_activity):
- """Set 'component_label' to have a fixed fugacity"""
- cdef int c_index
- c_index = self.database.component_label_to_id(component_label)
- self.constraints.add_fixed_activity_component(c_index, log_activity)
-
- # Inert volume
- # ------------
-
- def set_inert_volume_fraction(self, volume_fraction_inert):
- """Set the volume fraction of inert materials"""
- self.constraints.set_inert_volume_fraction(volume_fraction_inert)
-
-cdef class SpecMiCPFormulation(SpecMiCPConstraints):
- """The formulation of a problem"""
- def __cinit__(self, DatabaseManager database):
- self.formulation = new Formulation()
- def __dealloc__(self):
- del self.formulation
-
- def set_mass_solution(self, mass_solution):
- """Set the mass of the solution"""
- self.formulation.set_mass_solution(mass_solution)
- def add_aqueous_species(self, label, concentration):
- """Add an aqueous species to the system.
-
- An aqueous species can be in that case a component or a secondary
- aqueous species.
-
- 'concentration' is in moles per volume
- """
- self.formulation.add_aqueous_species(label, concentration)
- def add_mineral(self, label, concentration):
- """Add a mineral species to the system.
-
- The mineral can be governed by equilibrium or by kinetics.
-
- 'concentration' is in moles per volume
- """
- self.formulation.add_mineral(label, concentration)
- def keep_component(self, label):
- """Keep the component 'label' in the database
- even if it does not exist in the initial system.
-
- This must be used if the component will be used later in the computation
- """
- self.formulation.keep_component(label)
- def set_list_minerals(self, list_minerals):
- """Set the list of minerals at equilibrium
-
- If this function is not called, or the size of the list is zero,
- all minerals in the database will be used.
- """
- cdef vector[string] list = list_minerals
- self.formulation.set_minerals_list(list)
-
- def initialize_system(self):
- """Initialize the system by dissolving the formulation"""
- cdef Dissolver* dissolver = new Dissolver(self.database.get_raw_db())
- cdef VectorXd total_conc = dissolver.dissolve(dereference(self.formulation))
- self._get().set_total_concentrations(total_conc)
- del dissolver
diff --git a/cython/specmicp/database.pxd b/cython/specmicp/database.pxd
deleted file mode 100644
index a2a2e13..0000000
--- a/cython/specmicp/database.pxd
+++ /dev/null
@@ -1,130 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-from libcpp.string cimport string
-from libcpp.vector cimport vector
-from libcpp.map cimport map as cmap
-from libcpp cimport bool
-from memory cimport shared_ptr
-from eigen cimport MatrixXd, VectorXd
-
-
-# The raw container
-cdef extern from "database/data_container.hpp" namespace "specmicp::database":
- cdef cppclass DataContainer:
- int water_index();
- int electron_index();
-
- # basis
- # -----
- int nb_component()
- int nb_aqueous_components()
- int get_id_component(string)
- string get_label_component(int)
-
- # aqueous
- # -------
- int nb_aqueous()
- int get_id_aqueous(string)
- string get_label_aqueous(int)
- double nu_aqueous(int, int)
- double logk_aqueous(int)
-
- # mineral
- # -------
- int nb_mineral()
- int get_id_mineral(string)
- string get_label_mineral(int)
- double nu_mineral(int, int)
- double logk_mineral(int)
- double molar_mass_mineral(int)
- double molar_volume_mineral(int)
-
- int nb_mineral_kinetic()
- int get_id_mineral_kinetic(string)
- string get_label_mineral_kinetic(int)
- double nu_mineral_kinetic(int, int)
- double logk_mineral_kinetic(int)
- double molar_mass_mineral_kinetic(int)
- double molar_volume_mineral_kinetic(int)
-
- # gas
- # ---
- int nb_gas()
- int get_id_gas(string)
- string get_label_gas(int)
- double nu_gas(int, int)
- double logk_gas(int)
-
-
-# The database manager
-# Used to create and modify the database
-cdef extern from "database/database.hpp" namespace "specmicp::database":
- cdef cppclass Database:
- # cython-cpp interface - list of methods that we can access
- # Database should be the only module accessible from python
- Database()
- Database(shared_ptr[DataContainer])
- Database(string) except +
- void parse_database(string) except +
- shared_ptr[DataContainer] get_database()
- void swap_components(cmap[string, string]) except +
- void minerals_keep_only(vector[string]) except +
- bool is_valid()
- void remove_gas_phases()
- void add_gas_phases(string)
- void remove_solid_phases()
- void add_solid_phases(string)
- void remove_sorbed_species()
- void add_sorbed_species(string)
- # The following methods are from
- # specmicp::database::DatabaseModule
- int component_label_to_id(string)
- int safe_component_label_to_id(string) except +
- int aqueous_label_to_id(string)
- int safe_aqueous_label_to_id(string) except +
- int mineral_label_to_id(string)
- int safe_mineral_label_to_id(string) except +
- int mineral_kinetic_label_to_id(string)
- int safe_mineral_kinetic_label_to_id(string) except +
- int gas_label_to_id(string)
- int safe_gas_label_to_id(string) except +
-
-
-# header
-cdef class DatabaseManager:
- """ The Python database handler
-
- Use this class for checking values in the database
- or switching basis/dropping minerals or components...
- """
- cdef Database *database
- cdef void init_database(self, shared_ptr[DataContainer] raw_db)
- cdef shared_ptr[DataContainer] container
- cdef shared_ptr[DataContainer] get_raw_db(self)
- cdef DataContainer* _get(self)
diff --git a/cython/specmicp/database.pyx b/cython/specmicp/database.pyx
deleted file mode 100644
index 61fafe2..0000000
--- a/cython/specmicp/database.pyx
+++ /dev/null
@@ -1,470 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-from libcpp.map cimport map as cmap
-from libcpp.pair cimport pair
-
-from memory cimport shared_ptr
-from database cimport Database, DataContainer
-
-
-# Used to indicate that something does not exist
-cdef enum:
- no_species = -1
-
-cdef class DatabaseManager:
- """ The Python database handler
-
- Use this class for checking values in the database
- or switching basis/dropping minerals or components...
- """
- def __cinit__(self, bytes filepath):
- """filepath is the path to the database file"""
- if filepath:
- self.database = new Database(<string> filepath)
- else:
- self.database = new Database()
- self.container = self.database.get_database()
- def __dealloc__(self):
- del self.database
- cdef void init_database(self, shared_ptr[DataContainer] raw_db):
- del self.database
- self.database = new Database(raw_db)
- self.container = self.database.get_database()
- cdef shared_ptr[DataContainer] get_raw_db(self):
- return self.container
- cdef DataContainer* _get(self):
- return self.container.get()
-
- def is_valid(self):
- """Return true of the database is valid.
-
- If it isn't valid, something went wrong.
- """
- return self.database.is_valid();
-
-
- def remove_sorbed_species(self):
- """Remove all the sorbed species in the database."""
- self.database.remove_sorbed_species()
-
- def add_sorbed_species(self, bytes input_sorbed):
- """ Add sorbed species in the database
-
- 'input_sporbed' is a JSON list of sorbed species formatted as in the
- database
- """
- self.database.add_sorbed_species(input_sorbed)
-
- # --------- #
- # Component #
- # --------- #
-
- property nb_component:
- """The number of component in the database."""
- def __get__(self): return self._get().nb_component()
-
- def component_check_bounds(self, int idc):
- """Check if 'idc' is a correct index for a component.
-
- Raises a ValueError if it is not correct."""
- if (idc >= self.nb_component or idc < 0):
- raise ValueError("'"+str(idc)+
- "' is not a valid index for a component")
-
- # labels and id
- # --------------
- def component_label_to_id(self, bytes comp):
- """ Return the id of a component."""
- cdef int ans = self.database.component_label_to_id(comp)
- if (ans == no_species):
- raise ValueError("Species : '"+comp.decode()+"' is not a component.")
- return ans
- def component_id_to_label(self, int idc):
- """ Return the label of a component."""
- if (idc >= self.nb_component):
- raise ValueError("'"+str(idc)+
- "' is not a valid index for a component")
- return bytes(self._get().get_label_component(idc))
-
- def print_basis(self):
- """Print the components in the basis, with their ID"""
- print("The basis is :")
- cdef int i
- for i in range(self.nb_component):
- print(" - "+str(i)+" : "+bytes(self._get().get_label_component(i)).decode())
-
- # basis switch
- # ------------
-
- def swap_components(self, dict swapping):
- """Swap components in the basis
-
- swapping is a dictionnary where the keys are the labels of the
- components to replace and the values are the labels of the secondary
- species to add in the basis.
-
- Raise value errors if the labels are invalid
- """
- cdef cmap[string,string] input_map
- cdef int idsp
- for (key, value) in swapping.items():
- idsp = self.component_label_to_id(key)
- if (idsp == no_species):
- raise ValueError("'"+key.decode()+"' is not a valid component.")
- idsp = self.aqueous_label_to_id(value)
- if (idsp == no_species):
- raise ValueError("'"+key.decode()+
- "' is not a valid secondary aqueous species.")
- input_map.insert(pair[string, string](key, value))
- self.database.swap_components(input_map)
-
- # --------------- #
- # Aqueous species #
- # --------------- #
-
- property nb_aqueous:
- """The number of secondary aqueous species in the database"""
- def __get__(self): return self._get().nb_aqueous()
-
- def aqueous_check_bounds(self, int ida):
- """Check if 'ida' is a correct index for a secondary aqueous species.
-
- Raises a ValueError if it is not correct."""
- if (ida >= self.nb_aqueous or ida < 0):
- raise ValueError("'"+str(ida)+
- "' is not a valid index for a secondary aqueous species")
-
- # labels and id
- # -------------
- def aqueous_id_to_label(self, int ids):
- self.aqueous_check_bounds(ids)
- return bytes(self._get().get_label_aqueous(ids))
-
- def aqueous_label_to_id(self, bytes aqueous):
- """ Return the id of a secondary aqueous species"""
- cdef int ans = self.database.aqueous_label_to_id(aqueous)
- if (ans == no_species):
- raise ValueError("Species : '"+aqueous.decode()+
- "' is not a secondary aqueous species.")
- return ans
-
- def print_aqueous(self):
- """ Print the secondary species"""
- print("The secondary aqueous species are :")
- cdef int i
- for i in range(self.nb_aqueous):
- print(" - "+str(i)+" : "+bytes(self._get().get_label_aqueous(i)).decode())
-
- # properties
- # ----------
-
- def nu_aqueous(self, int ids, int idc):
- """Return stoichiometric coefficient of a secondary aqueous species"""
- self.aqueous_check_bounds(ids)
- self.component_check_bounds(idc)
- return self._get().nu_aqueous(ids, idc)
- def l_nu_aqueous(self, bytes aqueous, bytes component):
- """Return stoichiometric coefficient of a secondary aqueous species"""
- return self._get().nu_aqueous(self.aqueous_label_to_id(aqueous),
- self.component_label_to_id(component))
-
- def logk_aqueous(self, int ids):
- """Return the equilibrium constant of a secondary aqueous species"""
- self.aqueous_check_bounds(ids)
- return self._get().logk_aqueous(ids)
- def l_logk_aqueous(self, bytes aqueous):
- """Return the equilibrium constant of a secondary aqueous species"""
- return self._get().logk_aqueous(self.aqueous_label_to_id(aqueous))
-
- # ------------ #
- # Solid phases #
- # ------------ #
-
- def remove_solid_phases(self):
- """Remove all the solid phases in the database.
- """
- self.database.remove_solid_phases()
-
- def add_solid_phases(self, bytes input_solid_phases):
- """Add some solid phases in the database.
-
- 'input_sorbed' is a JSON list of minerals formatted as in the database
- """
- self.database.add_solid_phases(input_solid_phases)
-
- # Equilibrium
- # =======
-
- property nb_mineral:
- """The number of mineral in the database"""
- def __get__(self):
- return self._get().nb_mineral()
-
- def mineral_check_bounds(self, int idm):
- """Check if 'idm' is a correct index for a mineral.
-
- Raises a ValueError if it is not correct."""
- if (idm >= self.nb_mineral or idm < 0):
- raise ValueError("'"+str(idm)+
- "' is not a valid index for a mineral")
-
-
- # labels and id
- # -------------
-
- def mineral_id_to_label(self, int idm):
- """Return the label of a mineral."""
- self.mineral_check_bounds(idm)
- return bytes(self._get().get_label_mineral(idm))
-
- def mineral_label_to_id(self, bytes mineral):
- """ Return the id of a mineral"""
- ans = self.database.mineral_label_to_id(mineral)
- if (ans == no_species):
- raise ValueError("Species : '"+mineral.decode()+
- "' is not a solid phase at equilibrium in the database.")
- return ans
-
- def print_minerals(self):
- """ Print the solid phases at equilibrium"""
- print("The solid phases at equilibrium are :")
- cdef int i
- for i in range(self.nb_mineral):
- print(" - "+str(i)+" : "+bytes(self._get().get_label_mineral(i)).decode())
-
- def minerals_keep_only(self, list_mineral_to_keep):
- """Keep only the solid phases in 'list_mineral_to_keep'"""
- # we first verify that the list is valid
- for label in list_mineral_to_keep:
- self.mineral_label_to_id(label) # just check that it is not raising any error
- self.database.minerals_keep_only(list_mineral_to_keep)
-
- # properties
- # ----------
-
- def logk_mineral(self, int idm):
- """Return the equilibrium constant of a solid phase"""
- self.mineral_check_bounds(idm)
- return self._get().logk_mineral(idm)
- def l_logk_mineral(self, bytes mineral):
- """Return the equilibrium constant of a solid phase"""
- return self._get().logk_mineral(self.mineral_label_to_id(mineral))
-
- def nu_mineral(self, int idm, int idc):
- """Return stoichometric coefficient of a mineral"""
- self.mineral_check_bounds(idm)
- self.component_check_bounds(idc)
- return self._get().nu_mineral(idm, idc)
- def l_nu_mineral(self, bytes mineral, bytes component):
- """Return stoichometric coefficient of a mineral"""
- return self._get().nu_mineral(self.mineral_label_to_id(mineral),
- self.component_label_to_id(component))
-
- def molar_mass_mineral(self, int idm):
- """Return the molar mass (kg/mol) of mineral 'idm'"""
- self.mineral_check_bounds(idm)
- return self._get().molar_mass_mineral(idm)
- def l_molar_mass_mineral(self, bytes mineral):
- """Return the molar mass (kg/mol) of 'mineral'"""
- return self.molar_mass_mineral(self.mineral_label_to_id(mineral))
-
- def molar_volume_mineral(self, int idm):
- """Return the molar volume (m^3/mol) of mineral 'idm'"""
- self.mineral_check_bounds(idm)
- return self._get().molar_volume_mineral(idm)
- def l_molar_volume_mineral(self, bytes mineral):
- """Return the molar volume (m^3/mol) of 'mineral'"""
- return self.molar_volume_mineral(self.mineral_label_to_id(mineral))
-
- def density_mineral(self, int idm):
- """Return the density (kg/m^3) of a mineral 'idm'"""
- return (self._get().molar_mass_mineral(idm)
- / self._get().molar_volume_mineral(idm))
- def l_density_mineral(self, bytes mineral):
- """Return the density (kg/m^3) of a mineral 'idm'"""
- return self.density_mineral(
- self.mineral_label_to_id(mineral))
-
- # Kinetic
- # ===========
-
- property nb_mineral_kinetic:
- """The number of mineral governed by kinetics in the database"""
- def __get__(self):
- return self._get().nb_mineral_kinetic()
-
- def mineral_kinetic_check_bounds(self, int idm):
- """Check if 'idm' is a correct index for a kinetic mineral.
-
- Raises a ValueError if it is not correct."""
- if (idm >= self.nb_mineral_kinetic or idm < 0):
- raise ValueError("'"+str(idm)+
- "' is not a valid index for a kinetic mineral")
-
-
- # labels and id
- # -------------
-
- def mineral_kinetic_id_to_label(self, int idm):
- """Return the label of a mineral."""
- self.mineral_kinetic_check_bounds(idm)
- return bytes(self._get().get_label_mineral_kinetic(idm))
-
- def mineral_kinetic_label_to_id(self, bytes mineral):
- """ Return the id of a mineral governed by kinetics"""
- ans = self.database.mineral_kinetic_label_to_id(mineral)
- if (ans == no_species):
- raise ValueError("Species : '"+mineral.decode()+
- "' is not a solid phase at equilibrium in the database.")
- return ans
-
-
- def print_minerals_kinetic(self):
- """ Print the solid phases governed by kinetic"""
- print("The solid phases governed by kinetics law are :")
- cdef int i
- for i in range(self.nb_mineral_kinetic):
- print(" - "+str(i)+" : "+bytes(self._get().get_label_mineral_kinetic(i)).decode())
-
- # properties
- # ----------
-
- def logk_mineral_kinetic(self, int idm):
- """Return the equilibrium constant of a solid phase"""
- self.mineral_kinetic_check_bounds(idm)
- return self._get().logk_mineral_kinetic(idm)
- def l_logk_mineral_kinetic(self, bytes mineral):
- """Return the equilibrium constant of a solid phase"""
- return self._get().logk_mineral_kinetic(
- self.mineral_kinetic_label_to_id(mineral))
-
- def nu_mineral_kinetic(self, int idm, int idc):
- """Return stoichometric coefficient of a mineral"""
- self.mineral_kinetic_check_bounds(idm)
- self.component_check_bounds(idc)
- return self._get().nu_mineral_kinetic(idm, idc)
- def l_nu_mineral_kinetic(self, bytes mineral, bytes component):
- """Return stoichometric coefficient of a mineral"""
- return self._get().nu_mineral_kinetic(
- self.mineral_kinetic_label_to_id(mineral),
- self.component_label_to_id(component))
-
- def molar_mass_mineral_kinetic(self, int idm):
- """Return the molar mass (kg/mol) of mineral 'idm'"""
- self.mineral_kinetic_check_bounds(idm)
- return self._get().molar_mass_mineral_kinetic(idm)
- def l_molar_mass_mineral_kinetic(self, bytes mineral):
- """Return the molar mass (kg/mol) of 'mineral'"""
- return self.molar_mass_mineral_kinetic(
- self.mineral_kinetic_label_to_id(mineral))
-
- def molar_volume_mineral_kinetic(self, int idm):
- """Return the molar volume (m^3/mol) of mineral 'idm'"""
- self.mineral_kinetic_check_bounds(idm)
- return self._get().molar_volume_mineral_kinetic(idm)
- def l_molar_volume_mineral_kinetic(self, bytes mineral):
- """Return the molar volume (m^3/mol) of 'mineral'"""
- return self.molar_volume_mineral_kinetic(
- self.mineral_kinetic_label_to_id(mineral))
-
- def density_mineral_kinetic(self, int idm):
- """Return the density (kg/m^3) of a mineral 'idm'"""
- return (self._get().molar_mass_mineral_kinetic(idm)
- / self._get().molar_volume_mineral_kinetic(idm))
- def l_density_mineral_kinetic(self, bytes mineral):
- """Return the density (kg/m^3) of a mineral 'idm'"""
- return self.density_mineral_kinetic(
- self.mineral_kinetic_label_to_id(mineral))
-
-
- # ========
- # Gas
- # ========
-
- property nb_gas:
- """The number of gas in the database"""
- def __get__(self):
- return self._get().nb_gas()
-
- def gas_check_bounds(self, int idg):
- """Check if idg is a correct index for a gas"""
- if (idg >= self.nb_gas or idg < 0):
- raise ValueError("'"+str(idg)+
- "' is not a valid index for a gas")
-
- def gas_id_to_label(self, int idg):
- """Return the label of a gas."""
- self.gas_check_bounds(idg)
- return bytes(self._get().get_label_gas(idg))
-
- def gas_label_to_id(self, bytes gas):
- """ Return the id of a mineral"""
- ans = self.database.gas_label_to_id(gas)
- if (ans == no_species):
- raise ValueError("Species : '"+gas.decode()+
- "' is not a gas in the database.")
- return ans
-
- def remove_gas_phases(self):
- """Remove all the gas species in the database."""
- self.database.remove_gas_phases()
-
- def add_gas_phases(self, bytes input_gas_phases):
- """Add some gas into the database.
-
- 'input_gas_phases' is a JSON list of gas formatted as in the database.
- """
- self.database.add_gas_phases(input_gas_phases)
-
- def nu_gas(self, int idg, int idc):
- """Return the stoichiometric coefficient of 'idc' in 'idg' dissolution
- reaction."""
- self.gas_check_bounds(idg)
- self.component_check_bounds(idc)
- return self._get().nu_gas(idg, idc)
-
- def l_nu_gas(self, bytes gas, bytes component):
- """Return the stoihiometric coefficient of 'component' in the 'gas'
- dissolution reaction."""
- return self._get().nu_gas(self.gas_label_to_id(gas),
- self.component_label_to_id(component))
-
- def logk_gas(self, int idg):
- """Return the equilibrium constant of a gas"""
- self.gas_check_bounds(idg)
- if (idg >= self.nb_gas or idg < 0):
- raise ValueError("Index : '"+str(idg)
- +"'is not valid for a gas.")
- return self._get().logk_mineral(idg)
-
- def l_logk_gas(self, bytes gas):
- """Return the equilibrium constant of a gas"""
- return self._get().logk_gas(self.gas_label_to_id(gas))
\ No newline at end of file
diff --git a/cython/specmicp/init_log.hpp b/cython/specmicp/init_log.hpp
deleted file mode 100644
index ba11b17..0000000
--- a/cython/specmicp/init_log.hpp
+++ /dev/null
@@ -1,70 +0,0 @@
-/*-------------------------------------------------------------------------------
-
-Copyright (c) 2014,2015 F. Georget <fabieng@princeton.edu>, Princeton University
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation and/or
-other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-may be used to endorse or promote products derived from this software without
-specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
------------------------------------------------------------------------------*/
-
-#ifndef SPECMICP_CYTHON_INITLOG_HPP
-#define SPECMICP_CYTHON_INITLOG_HPP
-
-#include "utils/log.hpp"
-#include <iostream>
-
-namespace specmicp {
-
-
-inline void init_logger_cout_debug() {
- init_logger(&std::cout, specmicp::logger::Debug);
-}
-
-inline void init_logger_cout_warning() {
- init_logger(&std::cout, specmicp::logger::Warning);
-}
-
-inline void init_logger_cout_error() {
- init_logger(&std::cout, specmicp::logger::Error);
-}
-
-inline void init_logger_cerr_debug() {
- init_logger(&std::cerr, specmicp::logger::Debug);
-}
-
-inline void init_logger_cerr_warning() {
- init_logger(&std::cerr, specmicp::logger::Warning);
-}
-
-inline void init_logger_cerr_error() {
- init_logger(&std::cerr, specmicp::logger::Error);
-}
-
-
-
-} // end namespace specmicp
-
-#endif // SPECMICP_CYTHON_INITLOG_HPP
diff --git a/cython/specmicp/is_solver_successful.hpp b/cython/specmicp/is_solver_successful.hpp
deleted file mode 100644
index e4ed6f4..0000000
--- a/cython/specmicp/is_solver_successful.hpp
+++ /dev/null
@@ -1,60 +0,0 @@
-/*-------------------------------------------------------------------------------
-
-Copyright (c) 2014,2015 F. Georget <fabieng@princeton.edu>, Princeton University
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation and/or
-other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-may be used to endorse or promote products derived from this software without
-specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
------------------------------------------------------------------------------*/
-
-
-#ifndef SPECMICP_CYTHON_SUCCESSFUL_SOLVER
-#define SPECMICP_CYTHON_SUCCESSFUL_SOLVER
-
-#include "micpsolver/micpsolver_structs.hpp"
-#include <type_traits>
-
-// just for cython
-
-namespace specmicp {
-namespace micpsolver {
-
-//! \brief Return true if the solver is successful
-inline bool is_solver_successful(MiCPSolverReturnCode return_code)
-{
- return (return_code > MiCPSolverReturnCode::Success);
-}
-
-//! \brief Cast the return code to an int
-inline std::underlying_type<MiCPSolverReturnCode>::type cast_return_code(MiCPSolverReturnCode return_code)
-{
- return static_cast<std::underlying_type<MiCPSolverReturnCode>::type>(return_code);
-}
-
-} // end namespace micpsolver
-} // end namespace specmicp
-
-#endif //SPECMICP_CYTHON_SUCCESSFUL_SOLVER
diff --git a/cython/specmicp/logger.pxd b/cython/specmicp/logger.pxd
deleted file mode 100644
index 155e2d2..0000000
--- a/cython/specmicp/logger.pxd
+++ /dev/null
@@ -1,35 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-cdef extern from "init_log.hpp" namespace "specmicp":
- void c_init_looger_cout_debug "specmicp::init_logger_cout_debug" ()
- void c_init_logger_cout_warning "specmicp::init_logger_cout_warning" ()
- void c_init_logger_cout_error "specmicp::init_logger_cout_error" ()
- void c_init_logger_cerr_debug "specmicp::init_logger_cerr_debug" ()
- void c_init_logger_cerr_warning "specmicp::init_logger_cerr_warning" ()
- void c_init_logger_cerr_error "specmicp::init_logger_cerr_error" ()
diff --git a/cython/specmicp/logger.pyx b/cython/specmicp/logger.pyx
deleted file mode 100644
index 0335e74..0000000
--- a/cython/specmicp/logger.pyx
+++ /dev/null
@@ -1,47 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-cimport logger as lg
-
-def init_logger_cout_debug():
- lg.c_init_logger_cout_debug()
-
-def init_logger_cout_warning():
- lg.c_init_logger_cout_warning()
-
-def init_logger_cout_error():
- lg.c_init_logger_cout_error()
-
-def init_logger_cerr_debug():
- lg.c_init_logger_cerr_debug()
-
-def init_logger_cerr_warning():
- lg.c_init_logger_cerr_warning()
-
-def init_logger_cerr_error():
- lg.c_init_logger_cerr_error()
diff --git a/cython/specmicp/set_units.hpp b/cython/specmicp/set_units.hpp
deleted file mode 100644
index 9123954..0000000
--- a/cython/specmicp/set_units.hpp
+++ /dev/null
@@ -1,48 +0,0 @@
-/*-------------------------------------------------------------------------------
-
-Copyright (c) 2014,2015 F. Georget <fabieng@princeton.edu>, Princeton University
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation and/or
-other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-may be used to endorse or promote products derived from this software without
-specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
------------------------------------------------------------------------------*/
-
-#ifndef SPECMICP_CYTHON_SETUNITS
-#define SPECMICP_CYTHON_SETUNITS
-
-#include "physics/units.hpp"
-
-namespace specmicp {
-namespace units {
-
-inline void set_meter(LengthUnit& length) {length = LengthUnit::meter;}
-inline void set_decimeter(LengthUnit& length) {length = LengthUnit::decimeter;}
-inline void set_centimeter(LengthUnit& length) {length = LengthUnit::centimeter;}
-
-} // end namespace units
-} // end namespace specmicp
-
-#endif
diff --git a/cython/specmicp/solution.pxd b/cython/specmicp/solution.pxd
deleted file mode 100644
index f5cd3eb..0000000
--- a/cython/specmicp/solution.pxd
+++ /dev/null
@@ -1,102 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-from libcpp cimport bool
-from memory cimport shared_ptr
-from database cimport DataContainer, DatabaseManager
-from units cimport UnitsSet
-from eigen cimport VectorXd
-
-# The solution
-# -------------
-# note: access is restrictive since the user should use
-# the extractor class to acces the data
-cdef extern from "specmicp/adimensional/adimensional_system_solution.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemSolution:
- AdimensionalSystemSolution()
- AdimensionalSystemSolution(const AdimensionalSystemSolution&)
- bool is_valid
-
-# The solution extractor
-# ----------------------
-cdef extern from "specmicp/adimensional/adimensional_system_solution_extractor.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemSolutionExtractor:
- AdimensionalSystemSolutionExtractor(
- const AdimensionalSystemSolution&,
- shared_ptr[DataContainer],
- UnitsSet
- )
-
- double volume_fraction_water()
- double density_water()
- double saturation_water()
- double saturation_gas_phase()
- double porosity()
- double pE()
- double Eh()
- double molality_component(int)
- double activity_component(int)
- double volume_fraction_mineral(int)
- double mole_concentration_mineral(int)
- double mass_concentration_mineral(int)
- double saturation_index(int)
- double free_surface_concentration()
- double ionic_strength()
- double pH()
- double molality_aqueous(int)
- double activity_aqueous(int)
- double fugacity_gas(int)
- double molality_sorbed_species(int)
- double total_aqueous_concentration(int)
- double total_solid_concentration(int)
- double total_immobile_concentration(int)
- double volume_fraction_inert()
- VectorXd get_main_variables()
- shared_ptr[DataContainer] get_database()
-
-
-# Cython wrapper
-# --------------
-# the extractor only contains a reference to the solution
-# so we need to store the solution also
-cdef class SpecMiCPSolution:
- cdef AdimensionalSystemSolution* solution
- cdef AdimensionalSystemSolutionExtractor* extractor
- cdef DatabaseManager db
-
- cdef void set_solution(
- self,
- const AdimensionalSystemSolution& solution,
- shared_ptr[DataContainer] database,
- UnitsSet units_set
- )
- cdef AdimensionalSystemSolution* _get(self)
- cdef VectorXd get_main_variables(self)
-
-
diff --git a/cython/specmicp/solution.pyx b/cython/specmicp/solution.pyx
deleted file mode 100644
index c3f2318..0000000
--- a/cython/specmicp/solution.pyx
+++ /dev/null
@@ -1,208 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-from solution cimport SpecMiCPSolution
-from cython.operator cimport dereference
-from specmicp.database cimport DataContainer, DatabaseManager
-from units cimport UnitsSet
-
-cdef class SpecMiCPSolution:
- """Contain a solution from the SpecMiCP solver
-
- It correspond to the AdimensionalSystemSolutionExtractor of the c++ API
-
- This class should only be created by the SpecMiCP solver.
- """
-
- def __dealloc__(self):
- if self.extractor:
- del self.extractor
- if self.solution:
- del self.solution
- cdef void set_solution(
- self,
- const AdimensionalSystemSolution& solution,
- shared_ptr[DataContainer] database,
- UnitsSet units_set
- ):
- """Set the solution -- only callable from cython code !"""
- self.solution = new AdimensionalSystemSolution(solution)
- self.extractor = new AdimensionalSystemSolutionExtractor(
- dereference(self.solution),
- database,
- units_set
- )
- self.db = DatabaseManager(b"")
- self.db.init_database(self.extractor.get_database())
-
- cdef AdimensionalSystemSolution* _get(self):
- """Return the solution, only callable from cython code"""
- return self.solution
-
- cdef VectorXd get_main_variables(self):
- """Return the vector of main variables"""
- return self.extractor.get_main_variables()
-
- # water and gas volume fraction
- # -----------------------------
- def volume_fraction_water(self):
- """Return the volume fraction of water"""
- return self.extractor.volume_fraction_water()
- def density_water(self):
- """Return the density of water (in the correct units)"""
- return self.extractor.density_water()
- def porosity(self):
- """Return the porosity"""
- return self.extractor.porosity()
- def saturation_water(self):
- """Return the saturation of the liquid phase"""
- return self.extractor.saturation_water()
- def saturation_gas_phase(self):
- """Return the saturation of the gas phase"""
- return self.extractor.saturation_gas_phase()
- def volume_fraction_inert(self):
- """Return the volume fraction of inert phases"""
- return self.extractor.volume_fraction_inert()
- # solution properties
- # -------------------
- def pE(self):
- """Return pE"""
- return self.extractor.pE()
- def Eh(self):
- """Return Eh"""
- return self.extractor.Eh()
- def pH(self):
- """Return the pH of the solution"""
- return self.extractor.pH()
- def ionic_strength(self):
- """Return the ionic strength of the solution"""
- return self.extractor.ionic_strength()
- # components
- def molality_component(self, index):
- """Return molality of component 'index'"""
- return self.extractor.molality_component(index)
- def l_molality_component(self, label):
- """Return molality of component 'label'"""
- idc = self.db.component_label_to_id(label)
- return self.extractor.molality_component(idc)
- def activity_component(self, index):
- """Return the molality of component 'index'"""
- return self.extractor.activity_component(index)
- def l_activity_component(self, label):
- """Return the molality of component 'label'"""
- idc = self.db.component_label_to_id(label)
- return self.extractor.activity_component(idc)
- # minerals
- # --------
- def volume_fraction_mineral(self, index):
- """Return the volume fraction of mineral 'index'"""
- return self.extractor.volume_fraction_mineral(index)
- def l_volume_fraction_mineral(self, label):
- """Return the volume fraction of mineral 'label'"""
- idm = self.db.mineral_label_to_id(label)
- return self.extractor.volume_fraction_mineral(idm)
- def mole_concentration_mineral(self, index):
- """Return the concentration (mol/V) of mineral 'index'"""
- return self.extractor.mole_concentration_mineral(index)
- def l_mole_concentration_mineral(self, label):
- """Return the concentration (mol/V) of mineral 'label'"""
- idm = self.db.mineral_label_to_id(label)
- return self.extractor.mole_concentration_mineral(idm)
- def mass_concentration_mineral(self, index):
- """Return the concentration (M/V) of mineral 'index'"""
- return self.extractor.mass_concentration_mineral(index)
- def l_mass_concentration_mineral(self, label):
- """Return the concentration (M/V) of mineral 'label'"""
- idm = self.db.mineral_label_to_id(label)
- return self.extractor.mass_concentration_mineral(label)
- def saturation_index(self, index):
- """Return the saturation index of mineral 'index'"""
- return self.extractor.saturation_index(index)
- def l_saturation_index(self, label):
- """Return the saturation index of mineral 'index'"""
- idm = self.db.mineral_label_to_id(label)
- return self.extractor.saturation_index(idm)
- # aqueous species
- # ---------------
- def molality_aqueous(self, index):
- """Return the molality of aqueous 'index'"""
- return self.extractor.molality_aqueous(index)
- def l_molality_aqueous(self, label):
- """Return the molality of aqueous 'index'"""
- ida= self.db.aqueous_label_to_id(label)
- return self.extractor.molality_aqueous(ida)
- def activity_aqueous(self, index):
- """Return the activity of aqueous 'index'"""
- return self.extractor.activity_aqueous(index)
- def l_activity_aqueous(self, label):
- """Return the activity of aqueous 'index'"""
- ida= self.db.aqueous_label_to_id(label)
- return self.extractor.activity_aqueous(ida)
- # gas
- # ---
- def fugacity_gas(self, index):
- """Return the fugacity of gas 'index'"""
- return self.extractor.fugacity_gas(index)
- # sorption model
- # --------------
- def concentration_free_surface_sites(self):
- """Return the concentration of free surface sites"""
- return self.extractor.free_surface_concentration()
- def molality_sorbed_species(self, index):
- """Return the molality of sorbed_species 'index'"""
- return self.extractor.molality_sorbed_species(index)
- # total concentrations
- # --------------------
- def total_aqueous_concentration(self, index):
- """Return the total aqueous concentration of component 'index'"""
- return self.extractor.total_aqueous_concentration(index)
- def l_total_aqueous_concentration(self, label):
- """Return the total aqueous concentration of component 'index'"""
- idc = self.db.component_label_to_id(label)
- return self.extractor.total_aqueous_concentration(idc)
- def total_solid_concentration(self, index):
- """Return the total solid concentration of component 'index'"""
- return self.extractor.total_solid_concentration(index)
- def l_total_solid_concentration(self, label):
- """Return the total solid concentration of component 'index'"""
- idc = self.db.component_label_to_id(label)
- return self.extractor.total_solid_concentration(idc)
- def total_immobile_concentration(self, index):
- """Return the total immobile (solid+sorbed) concentration of component
- 'index'"""
- return self.extractor.total_immobile_concentration(index)
- def l_total_immobile_concentration(self, label):
- """Return the total immobile (solid+sorbed) concentration of component
- 'label'"""
- idc = self.db.component_label_to_id(label)
- return self.extractor.total_immobile_concentration(idc)
-
-
- def get_database(self):
- """Return the database"""
- return self.db
diff --git a/cython/specmicp/solver.pxd b/cython/specmicp/solver.pxd
deleted file mode 100644
index 3aa591a..0000000
--- a/cython/specmicp/solver.pxd
+++ /dev/null
@@ -1,72 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-from libcpp.map cimport map as cmap
-from libcpp cimport bool
-from libcpp.string cimport string
-from eigen cimport VectorXd
-from memory cimport shared_ptr
-from database cimport DatabaseManager, DataContainer
-
-from solution cimport AdimensionalSystemSolution
-from constraints cimport AdimensionalSystemConstraints
-from solver_options cimport MiCPPerformance, AdimensionalSystemSolverOptions, AdimensionalSystemOptions, MiCPSolverOptions
-
-# The SpecMiCP Solver
-# -------------------
-cdef extern from "specmicp/adimensional/adimensional_system_solver.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemSolver:
- AdimensionalSystemSolver(
- shared_ptr[DataContainer],
- const AdimensionalSystemConstraints&
- )
- AdimensionalSystemSolver(
- shared_ptr[DataContainer],
- const AdimensionalSystemConstraints&,
- const AdimensionalSystemSolution&
- )
-
- MiCPPerformance solve(VectorXd&, bool) nogil except +,
- AdimensionalSystemSolution get_raw_solution(VectorXd&)
- void run_pcfm(VectorXd&)
- void initialise_variables(VectorXd&, double, cmap[string, double])
- void initialise_variables(VectorXd&, double, double)
-
- AdimensionalSystemSolverOptions& get_options() nogil # read-only
-
-# Wrapper to the solver
-# ---------------------
-cdef class SpecMiCPSolver:
- cdef DatabaseManager database
- cdef AdimensionalSystemSolver* solver
- cdef VectorXd* variables
- cdef bool is_solved
-
- cdef AdimensionalSystemSolverOptions* get_options(self) nogil
- cdef AdimensionalSystemOptions* get_system_options(self) nogil
- cdef MiCPSolverOptions* get_micpsolver_options(self) nogil
diff --git a/cython/specmicp/solver.pyx b/cython/specmicp/solver.pyx
deleted file mode 100644
index b5b79c0..0000000
--- a/cython/specmicp/solver.pyx
+++ /dev/null
@@ -1,255 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-from libcpp.map cimport map as cmap
-from libcpp.string cimport string
-from libcpp.utility cimport pair
-from solver cimport SpecMiCPSolver, AdimensionalSystemSolver
-from database cimport DatabaseManager
-from constraints cimport SpecMiCPConstraints, AdimensionalSystemConstraints
-from solver_options cimport MiCPSolverReturnCode, MiCPPerformance, is_solver_successful
-from solution cimport SpecMiCPSolution
-cimport units
-from cython.operator cimport dereference
-
-cdef class SpecMiCPSolver:
- def __cinit__(
- self,
- DatabaseManager database not None,
- SpecMiCPConstraints constraints not None,
- SpecMiCPSolution solution
- ):
- """Initialisation"""
- self.is_solved = False
- self.database = database
- if solution is None:
- self.solver = new AdimensionalSystemSolver(
- database.get_raw_db(),
- dereference(constraints._get())
- )
- else:
- self.solver = new AdimensionalSystemSolver(
- database.get_raw_db(),
- dereference(constraints._get()),
- dereference(solution._get())
- )
- self.variables = new VectorXd(solution.get_main_variables())
-
- def __dealloc__(self):
- if self.solver:
- del self.solver
- if self.variables:
- del self.variables
-
- cdef AdimensionalSystemSolverOptions* get_options(self) nogil:
- """Return the options"""
- return &(self.solver.get_options())
-
- cdef AdimensionalSystemOptions* get_system_options(self) nogil:
- """Return the options of the SpecMiCP program"""
- return &(self.solver.get_options().system_options)
-
- cdef MiCPSolverOptions* get_micpsolver_options(self) nogil:
- """Return the MiCPSolver options"""
- return &(self.solver.get_options().solver_options)
-
- def get_solution(self):
- """Return the solution"""
- if not self.solver:
- raise RuntimeError("No solver")
- if not self.is_solved:
- raise RuntimeError("No solution available")
- solution = SpecMiCPSolution()
- solution.set_solution(
- self.solver.get_raw_solution(dereference(self.variables)),
- self.database.get_raw_db(),
- self.solver.get_options().units_set
- )
- return solution
-
- def initialize_variables(self, water_saturation, log_molalities_component):
- """Initialize the variables
-
- The log_molalities_component can be
- - a double : the initial value gor the log_10 of the molalities
- - a dictionnary {"label component": log_molalities}
- """
- cdef cmap[string, double] map_comp
- if not self.variables:
- self.variables = new VectorXd()
- if hasattr(log_molalities_component, "items"):
- for (key, value) in log_molalities_component.items():
- map_comp.insert(pair[string, double](key, value))
- self.solver.initialise_variables(dereference(self.variables),
- float(water_saturation),
- map_comp)
- else:
- self.solver.initialise_variables(dereference(self.variables),
- float(water_saturation),
- float(log_molalities_component)
- )
-
- def solve(self, initialize=True):
- """Solve the problem"""
- cdef MiCPPerformance perf
- cdef bool init = initialize
- if not self.variables:
- self.variables = new VectorXd()
- with nogil:
- perf = self.solver.solve(dereference(self.variables), init)
- if not is_solver_successful(perf.return_code):
- raise RuntimeError("Error - the system cannot be solved.")
- self.is_solved = True
-
- # Options
- # =======
-
- # adimensionalsolver options
- # --------------------------
-
- def set_length_unit(self, length_unit):
- """Set the length unit"""
- if length_unit in ("m", "meter"):
- units.set_meter(self.get_options().units_set.length)
- elif length_unit in ("dm", "decimeter"):
- units.set_decimeter(self.get_options().units_set.length)
- elif length_unit in ("cm", "centimeter"):
- units.set_centimeter(self.get_options().units_set.length)
- else:
- raise ValueError("Unit : " + str(length_unit) + "is not recognized")
-
- def enable_restart(self):
- """Allow the solve to be restarted in case of failure"""
- self.get_options().allow_restart = True
- def disable_restart(self):
- """Failure to solve the problem is critical"""
- self.get_options().allow_restart = False
-
- def enable_pcfm(self):
- """Enable the positive continuous fraction method"""
- self.get_options().use_pcfm = True
- def disable_pcfm(self):
- """Disable the positive continuous fraction method"""
- self.get_options().use_pcfm = False
-
- # System options
- # ---------------
-
- def enable_non_ideality(self):
- """Enable the nonideality model of the aqueous solution"""
- self.get_system_options().non_ideality = True
- def disable_non_ideality(self):
- """Disable the nonideality model of the aqueous solution"""
- self.get_system_options().non_ideality = False
-
- def set_non_ideality_max_iterations(self, max_iterations):
- """Set the maximum iterations allowed for the non ideality model"""
- self.get_system_options().non_ideality_max_iter = int(max_iterations)
-
- def set_non_ideality_tolerance(self, tolerance):
- """Set the tolerance for the non ideality model"""
- self.get_system_options().non_ideality_tolerance = float(tolerance)
-
- def set_non_ideality_start_factor(self, start_factor):
- """A factor that governs the non-ideality computation"""
- self.get_system_options().start_non_ideality_computation = float(start_factor)
-
- def set_under_relaxation_factor(self, factor):
- """Set the under relaxtion factor """
- self.get_system_options().under_relaxation_factor = float(factor)
-
- def set_restart_concentration(self, log_molality):
- """Set the molality used to re-initialize the problem in case of failure"""
- self.get_system_options().restart_concentration = float(log_molality)
-
- def set_new_component_concentration(self, log_molality):
- """Set the concentration for a new component"""
- self.get_system_options().new_component_concentration = float(log_molality)
-
- def set_cutoff_total_concentrations(self, cutoff):
- """Set the cutoff for the total concentrations"""
- self.get_system_options().cutoff_total_concentration = float(cutoff)
-
- # MiCPSolver options
- # ------------------
-
- def set_tolerance(self, residuals_tol):
- """Set the residuals tolerance"""
- self.get_micpsolver_options().set_tolerance(residuals_tol)
- def set_tolerances(self, residuals_tol, step_tol):
- """"Set the residuals and the step tolerances"""
- self.get_micpsolver_options().set_tolerance(residuals_tol, step_tol)
-
- def set_maximum_iterations(self, max_iterations):
- """Set the maximum number of operations"""
- self.get_micpsolver_options().set_maximum_iterations(max_iterations)
-
- def set_maximum_step_length(self, max_step_length, max_iter_at_max_length=None):
- """Set the maximum step length"""
- if max_iter_at_max_length is not None:
- self.get_micpsolver_options().set_maximum_step_length(
- max_step_length, max_iter_at_max_length)
- else:
- self.get_micpsolver_options().set_maximum_step_length(
- max_step_length)
-
- def disable_descent_direction(self):
- """Disable the descent direction condition"""
- self.get_micpsolver_options().disable_descent_direction()
- def enable_descent_direction(self, factor, power):
- """Enable the descent direction condition"""
- self.get_micpsolver_options().enable_descent_direction(factor, power)
-
- def disable_condition_check(self):
- """Disable the descent direction"""
- self.get_micpsolver_options().disable_condition_check()
- def enable_condition_check(self, threshold):
- """Enable the condition check"""
- self.get_micpsolver_options().enable_condition_check(threshold)
-
- def disable_non_monotone_linesearch(self):
- """Disable the non monotone linesearch"""
- self.get_micpsolver_options().disable_non_monotone_linesearch()
- def enable_non_monotone_linesearch(self):
- """Enable the non monotone linesearch"""
- self.get_micpsolver_options().enable_non_monotone_linesearch()
-
- def disable_jacobian_scaling(self):
- """Disable the Jacobian scaling"""
- self.get_micpsolver_options().disable_scaling()
- def enable_jacobian_scaling(self):
- """Enable the Jacobian scaling"""
- self.get_micpsolver_options().enable_scaling()
-
- def disable_crashing(self):
- """Disable the crashing"""
- self.get_micpsolver_options().disable_crashing()
- def enable_crashing(self):
- """Enable the crashing"""
- self.get_micpsolver_options().enable_crashing()
diff --git a/cython/specmicp/solver_options.pxd b/cython/specmicp/solver_options.pxd
deleted file mode 100644
index e3ecc86..0000000
--- a/cython/specmicp/solver_options.pxd
+++ /dev/null
@@ -1,123 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-from libcpp cimport bool
-from units cimport UnitsSet
-
-cdef extern from "micpsolver/micpsolver_structs.hpp" namespace "specmicp::micpsolver":
- cdef cppclass MiCPSolverOptions:
- MiCPSolverOptions()
- int max_iter
- double fvectol
- double steptol
- double condition_limit
- double penalization_factor
- double maxstep
- int maxiter_maxstep
- double factor_descent_condition
- double power_descent_condition
- bool use_crashing
- double coeff_accept_newton_step
- bool use_scaling
- double factor_gradient_search_direction
- double projection_min_variable
- double threshold_stationary_point
- int max_factorization_step
-
- void set_maximum_iterations(int)
- void set_maximum_step_length(double)
- void set_maximum_step_length(double, int)
- void disable_descent_direction()
- void enable_descent_direction(double, double)
- void disable_condition_check()
- void enable_condition_check(double)
- void disable_non_monotone_linesearch()
- void enable_scaling()
- void disable_scaling()
- void enable_crashing()
- void disable_crashing()
- void enable_non_monotone_linesearch()
- void set_tolerance(double)
- void set_tolerance(double, double)
-
-
- cdef enum MiCPSolverReturnCode:
- LolItsNotSupposedToHappen "specmicp::micpsolver::MiCPSolverReturnCode::LolItsNotSupposedToHappen"
- MaxStepTakenTooManyTimes "specmicp::micpsolver::MiCPSolverReturnCode::MaxStepTakenTooManyTimes"
- FailedToSolveLinearSystem "specmicp::micpsolver::MiCPSolverReturnCode::FailedToSolveLinearSystem"
- MaxIterations "specmicp::micpsolver::MiCPSolverReturnCode::MaxIterations"
- StationaryPoint "specmicp::micpsolver::MiCPSolverReturnCode::StationaryPoint"
- NotConvergedYet "specmicp::micpsolver::MiCPSolverReturnCode::NotConvergedYet"
- Success "specmicp::micpsolver::MiCPSolverReturnCode::Success"
- ResidualMinimized "specmicp::micpsolver::MiCPSolverReturnCode::ResidualMinimized"
- ErrorMinimized "specmicp::micpsolver::MiCPSolverReturnCode::ErrorMinimized"
-
- cdef cppclass MiCPPerformance:
- MiCPPerformance()
- int nb_call_residuals
- int nb_call_jacobian
- int nb_factorization
- int nb_gradient_step
- int nb_crashing_iterations
- int nb_iterations
- bool max_taken
- int nb_max_taken
- int nb_consecutive_max_taken
- MiCPSolverReturnCode return_code
-
- cdef enum NCPfunction:
- penFB_function "specmicp::micpsolver::NCPfunction::penalizedFB"
- min_function "specmicp::micpsolver::NCPfunction::min"
-
-cdef extern from "is_solver_successful.hpp" namespace "specmicp::micpsolver":
- cdef bool is_solver_successful(MiCPSolverReturnCode)
- cdef int cast_return_code(MiCPSolverReturnCode)
-
-cdef extern from "specmicp/adimensional/adimensional_system_structs.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemOptions:
- bool non_ideality
- int non_ideality_max_iter
- double scaling_electron
- double non_ideality_tolerance
- double under_relaxation_factor
- double restart_concentration
- double new_component_concentration
- double start_non_ideality_computation
- double cutoff_total_concentration
-
-cdef extern from "specmicp/adimensional/adimensional_system_solver_structs.hpp" namespace "specmicp":
- cdef cppclass AdimensionalSystemSolverOptions:
- AdimensionalSystemSolverOptions()
- MiCPSolverOptions solver_options
- AdimensionalSystemOptions system_options
- UnitsSet units_set
- bool allow_restart
- bool use_pcfm
- bool force_pcfm
-
diff --git a/cython/specmicp/units.pxd b/cython/specmicp/units.pxd
deleted file mode 100644
index 146421a..0000000
--- a/cython/specmicp/units.pxd
+++ /dev/null
@@ -1,49 +0,0 @@
-#Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton
-#University #All rights reserved.
-#
-#Redistribution and use in source and binary forms, with or without
-#modification, are permitted provided that the following conditions are met:
-#
-#1. Redistributions of source code must retain the above copyright notice, this
-#list of conditions and the following disclaimer.
-#
-#2. Redistributions in binary form must reproduce the above copyright notice,
-#this list of conditions and the following disclaimer in the documentation
-#and/or other materials provided with the distribution.
-#
-#3. Neither the name of the copyright holder nor the names of its contributors
-#may be used to endorse or promote products derived from this software without
-#specific prior written permission.
-#
-#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-#ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-#DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-#FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-#DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-#SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-#CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-#OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-cdef extern from "physics/units.hpp" namespace "specmicp::units":
- cdef enum LengthUnit:
- meter "specmicp::units::LengthUnit::meter"
- decimeter "specmicp::units::LengthUnit::decimeter"
- centimeter "specmicp::units::LengthUnit::centimeter"
-
- cdef enum MassUnit:
- kilogram "specmicp::units::MassUnit::kilogram"
- gram "specmicp::units::MassUnit::gram"
-
- cdef cppclass UnitsSet:
- UnitsSet()
- MassUnit mass
- LengthUnit length
-
-# These are the function that allows us to overcome the "enum class" cython incompatibility
-cdef extern from "set_units.hpp" namespace "specmicp::units":
- void set_meter(LengthUnit&)
- void set_decimeter(LengthUnit&)
- void set_centimeter(LengthUnit&)
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 69ca1d7..9f8b24d 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -1,93 +1,78 @@
################## Tests ########################################
include(CatchTest)
set(PROJECT_TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR})
include_directories(${PROJECT_TEST_DIR})
add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND}) # make check is also valid
# Catch test
#===========
# MiCPSolver
# ----------
set(MICPSOLVER_TEST_DIR micpsolver)
add_catch_test(NAME micpsolver SOURCES
${MICPSOLVER_TEST_DIR}/test_micpsolver.cpp
${MICPSOLVER_TEST_DIR}/condition_number.cpp
${MICPSOLVER_TEST_DIR}/ncp_functions.cpp
${MICPSOLVER_TEST_DIR}/micpsolver.cpp
)
# ODEInt
# ----------
set(ODEINT_TEST_DIR odeint)
add_catch_test(NAME odeint SOURCES
${ODEINT_TEST_DIR}/test_odeint.cpp
${ODEINT_TEST_DIR}/butchertableau.cpp
${ODEINT_TEST_DIR}/embeddedrungekutta.cpp
)
# Database
# --------
add_subdirectory(database)
# Specmicp : Adim system
# ----------------------
add_catch_test(NAME specmicp_adim SOURCES
specmicp/adim/test_specmicp_adim.cpp
specmicp/adim/adimensional_system.cpp
specmicp/adim/adimensional_system_solver.cpp
specmicp/adim/adimensional_system_conditions.cpp
specmicp/adim/adimensional_system_problem_solver.cpp
specmicp/adim/adimensional_system_thermocarbo.cpp
specmicp/adim/adimensional_system_carboalu.cpp
specmicp/adim/adimensional_system_pcfm.cpp
specmicp/adim/adimensional_system_oxydoreduc.cpp
LINK_LIBRARIES specmicp_static specmicp_database_static
)
# Specmicp : Adim Kinetics
# ------------------------
set(ADIMKINETICS_TEST_DIR ${PROJECT_TEST_DIR}/specmicp/adim_kinetics)
add_catch_test(NAME specmicp_adim_kinetics SOURCES
${ADIMKINETICS_TEST_DIR}/test_specmicp_adim_kinetics.cpp
${ADIMKINETICS_TEST_DIR}/kinetics_variables.cpp
LINK_LIBRARIES specmicp_static specmicp_database_static
)
# Reactmicp
# ---------
add_subdirectory( reactmicp )
-
-# cython test
-# -----------
-
-# the cython tests are generated from the cython/CMakeLists.txt file
-
-if (SPECMICP_BUILD_CYTHON)
- add_test(NAME database_py
- COMMAND ${PYTHON_EXECUTABLE} "database.py"
- )
-
- add_test(NAME test_specmicp_py
- COMMAND ${PYTHON_EXECUTABLE} "test_specmicp.py"
- )
-endif()