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pdelab / modular-pnp

This repository contains a modularized implementation of the PNP solver in which functionalities are organized into Newton solver techniques, conversion methods between FEniCS and FASP, as well as geometric and parameter functionalities. An additional library specific to strictly PNP functionalities is also within.
https://thepnpsolver.github.io/
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This repository contains a modularized version of Penn State's CCMA Newton solver for the Poisson-Nernst-Planck system

TO COMPILE A SPECIFIC PROBLEM: In order to compile the code, copy the desired main.cpp file to ./main.cpp from the appropriate directory in ./problems/ and then run make followed by executing the ``PNP'' file

e.g. cp ./problems/voltage_benchmark/main.cpp ./main.cpp make ./PNP

TO CONFIGURE THE LIBRARY: CMake is used to link the required files and libraries. To ensure proper linking, create a CMakeLists.txt file in the current directory and run ``cmake .'' to build the appropriate files.

An example CMakeLists.txt file is below:

Begin CMakeLists.txt

Require CMake 2.8

cmake_minimum_required(VERSION 2.8)

set(PROJECT_NAME PNP) project(${PROJECT_NAME})

Set verbose output while testing CMake

set(CMAKE_VERBOSE_MAKEFILE 1)

Set CMake behavior

cmake_policy(SET CMP0004 OLD)

Get DOLFIN configuration data (DOLFINConfig.cmake must be in DOLFIN_CMAKE_CONFIG_PATH)

find_package(DOLFIN)

Need to get VTK config because VTK uses advanced VTK features which

mean it's not enough to just link to the DOLFIN target. See

http://www.vtk.org/pipermail/vtk-developers/2013-October/014402.html

find_package(VTK HINTS ${VTK_DIR} $ENV{VTK_DIR} NO_MODULE QUIET)

Default build type (can be overridden by user)

if (NOT CMAKE_BUILD_TYPE) set(CMAKE_BUILD_TYPE "RelWithDebInfo" CACHE STRING "Choose the type of build, options are: Debug MinSizeRel Release RelWithDebInfo." FORCE) endif()

Compiler definitions

add_definitions(${DOLFIN_CXX_DEFINITIONS})

Compiler flags

set(CMAKE_CXX_FLAGS "${DOLFIN_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")

Set FASP directories

set(FASP_DIR /usr/local/faspsolver) # must be set for each new build set(FASP4NS_DIR /usr/local/fasp4ns) # must be set for each new build

Include directories

set(FASP_INCLUDE_DIR ${FASP_DIR}/base/include) set(FASP4NS_INCLUDE_DIR ${FASP4NS_DIR}/include) include_directories(${DOLFIN_INCLUDE_DIRS} ${FASP_INCLUDE_DIR} ${FASP4NS_INCLUDE_DIR} ./include) include_directories(SYSTEM ${DOLFIN_3RD_PARTY_INCLUDE_DIRS})

Executable

add_executable(test_reading test_reading.cpp ./src/params.cpp ./src/domains.cpp) add_executable(test_ftof test_ftof.cpp ./src/ftof.cpp)

Target libraries

set(FASP_LIB ${FASP_DIR}/lib/libfasp.a) set(FASP4NS_LIB ${FASP4NS_DIR}/lib/libfasp4ns.a) target_link_libraries(test_reading ${DOLFIN_LIBRARIES} ${DOLFIN_3RD_PARTY_LIBRARIES} ${FASP_LIB} ${FASP4NS_LIB}) target_link_libraries(test_ftof ${DOLFIN_LIBRARIES} ${DOLFIN_3RD_PARTY_LIBRARIES} ${FASP_LIB} ${FASP4NS_LIB})

End CMakeLists.txt