Compare revisions

Xiaoran Zhou · Xiaoran Zhou · Xiaoran Zhou · Xiaoran Zhou · Xiaoran Zhou · Angela Kranz
--- a/.arc/.gitkeep
+++ b/.arc/.gitkeep
--- a/.arc/validation_packages.yml
+++ b/.arc/validation_packages.yml
+arc_specification: 2.0.0-draft
--- a/LICENSE
+++ b/LICENSE
--- a/assays/.gitkeep
+++ b/assays/.gitkeep
--- a/assays/Assay1/README.md
+++ b/assays/Assay1/README.md
--- a/assays/Assay1/dataset/.gitkeep
+++ b/assays/Assay1/dataset/.gitkeep
--- a/assays/Assay1/dataset/CPlantBox-isp/.gitignore
+++ b/assays/Assay1/dataset/CPlantBox-isp/.gitignore
+.project
+.cproject
+.pydevproject
+.settings/
+Debug/
+.vs
+CMakeFiles/
+a.out
+CPlantBox_Codeblocks_project/
+
+*.ipch *.db .vs/cpb/v15/.suo examples/PSP_infiltrationRedistribution1D/* 
+examples/Exudation/* /.vs /__pycache__/xylem_flux.cpython-35.pyc 
+/__pycache__/rb_tools.cpython-36.pyc 
+/__pycache__/rb_tools.cpython-35.pyc /__pycache__ 
+/CPlantBoxVS.vcxproj.user /CPlantBoxVS.vcxproj.filters 
+/CPlantBoxVS.vcxproj /CPlantBoxVS.sln /py_plantbox.so 
+/Report20180320-1455.diagsession /Debug /x64 *.vtp py_plantbox.so 
+examples/Coupling_PSP/__pycache__/
+# CMake clutter
+build-* Testing CMakeCache.txt CMakeFiles/ *.cmake *.a
+# auto-saved files
+*~
+examples/CMakeFiles/
+python/cpbvenv
+./src/CMakeFiles/*
+*/Makefile
+CMakeCache.txt
+cmake_install.cmake
+
+./src/libCPlantBox.a
+./examples/test_cplantbox
\ No newline at end of file
--- a/assays/Assay1/dataset/CPlantBox-isp/CMakeLists.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/CMakeLists.txt
+# build the CPlantBox library using CMake
+# Simply type cmake . && make
+# although out-of-source-builds are encouraged
+
+cmake_minimum_required (VERSION 2.8.12)
+project (CPlantBox)
+
+# set compiler options
+
+set(RELEASE_WARNING_OPTS "-Wall -Wunused -Wmissing-include-dirs -Wcast-align -Wno-sign-compare")
+set(DEBUG_WARNING_OPTS "-Wall -Wunused -Wmissing-include-dirs -Wcast-align")
+set(RELEASE_OPTS "-std=c++11 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -g0")
+set(CMAKE_CXX_FLAGS_RELEASE "${RELEASE_WARNING_OPTS} ${RELEASE_OPTS}")
+set(CMAKE_CXX_FLAGS_DEBUG "-std=c++11 -O0 -ggdb -Wall")
+
+# set default build type to release
+set(CMAKE_BUILD_TYPE Release)
+
+# add source directory to the include path
+include_directories(${PROJECT_SOURCE_DIR}/src)
+
+# add subdirectories
+add_subdirectory(src)
+add_subdirectory(examples)
+add_subdirectory(tutorial/jupyter)
--- a/assays/Assay1/dataset/CPlantBox-isp/CONTRIBUTING.md
+++ b/assays/Assay1/dataset/CPlantBox-isp/CONTRIBUTING.md
+# Naming Guidline
+Underlines used for parameter name
+Camel case (stylized as camelCase; also known as camel caps or more formally as medial capitals) is used for Class name (start with capital letter) and function name (start with lower case letter).
--- a/assays/Assay1/dataset/CPlantBox-isp/CPlantBox.cbp
+++ b/assays/Assay1/dataset/CPlantBox-isp/CPlantBox.cbp
+<?xml version="1.0" encoding="UTF-8"?>
+<CodeBlocks_project_file>
+	<FileVersion major="1" minor="6"/>
+	<Project>
+		<Option title="CPlantBox"/>
+		<Option makefile_is_custom="1"/>
+		<Option compiler="gcc"/>
+		<Option virtualFolders="CMake Files\;CMake Files\src\;CMake Files\examples\;CMake Files\python\;"/>
+		<Build>
+			<Target title="all">
+				<Option working_dir="/home/crootbox/CPlantBox"/>
+				<Option type="4"/>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 all"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="rebuild_cache">
+				<Option working_dir="/home/crootbox/CPlantBox"/>
+				<Option type="4"/>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 rebuild_cache"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="edit_cache">
+				<Option working_dir="/home/crootbox/CPlantBox"/>
+				<Option type="4"/>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 edit_cache"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="CPlantBox">
+				<Option output="/home/crootbox/CPlantBox/src/libCPlantBox.a" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/src"/>
+				<Option object_output="./"/>
+				<Option type="2"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+					<Add directory="/usr/include/python3.6m"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 CPlantBox"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="CPlantBox/fast">
+				<Option output="/home/crootbox/CPlantBox/src/libCPlantBox.a" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/src"/>
+				<Option object_output="./"/>
+				<Option type="2"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+					<Add directory="/usr/include/python3.6m"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 CPlantBox/fast"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="py_plantbox">
+				<Option output="/home/crootbox/CPlantBox/python/py_plantbox.so" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/src"/>
+				<Option object_output="./"/>
+				<Option type="3"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+					<Add directory="/usr/include/python3.6m"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 py_plantbox"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="py_plantbox/fast">
+				<Option output="/home/crootbox/CPlantBox/python/py_plantbox.so" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/src"/>
+				<Option object_output="./"/>
+				<Option type="3"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+					<Add directory="/usr/include/python3.6m"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 py_plantbox/fast"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/src/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="test_cplantbox">
+				<Option output="/home/crootbox/CPlantBox/examples/test_cplantbox" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/examples"/>
+				<Option object_output="./"/>
+				<Option type="1"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 test_cplantbox"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+			<Target title="test_cplantbox/fast">
+				<Option output="/home/crootbox/CPlantBox/examples/test_cplantbox" prefix_auto="0" extension_auto="0"/>
+				<Option working_dir="/home/crootbox/CPlantBox/examples"/>
+				<Option object_output="./"/>
+				<Option type="1"/>
+				<Option compiler="gcc"/>
+				<Compiler>
+					<Add directory="/home/crootbox/CPlantBox/src"/>
+				</Compiler>
+				<MakeCommands>
+					<Build command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 test_cplantbox/fast"/>
+					<CompileFile command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 &quot;$file&quot;"/>
+					<Clean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 clean"/>
+					<DistClean command="/usr/bin/make -f &quot;/home/crootbox/CPlantBox/examples/Makefile&quot;  VERBOSE=1 clean"/>
+				</MakeCommands>
+			</Target>
+		</Build>
+		<Unit filename="/home/crootbox/CPlantBox/examples/main.cpp">
+			<Option target="test_cplantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Leaf.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Leaf.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/LeafTropism.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/LeafTropism.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/ModelParameter.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/ModelParameter.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Organ.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Organ.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Plant.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Plant.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/PythonPlant.cpp">
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Root.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Root.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/RootTropism.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/RootTropism.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Seed.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Seed.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Stem.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/Stem.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/StemTropism.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/StemTropism.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/analysis.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/analysis.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/sdf.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/sdf.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/tinyxml2.cpp">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/tinyxml2.h">
+			<Option target="CPlantBox"/>
+			<Option target="py_plantbox"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/CMakeLists.txt">
+			<Option virtualFolder="CMake Files\"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/src/CMakeLists.txt">
+			<Option virtualFolder="CMake Files\src\"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/examples/CMakeLists.txt">
+			<Option virtualFolder="CMake Files\examples\"/>
+		</Unit>
+		<Unit filename="/home/crootbox/CPlantBox/python/CMakeLists.txt">
+			<Option virtualFolder="CMake Files\python\"/>
+		</Unit>
+	</Project>
+</CodeBlocks_project_file>
--- a/assays/Assay1/dataset/CPlantBox-isp/Doxyfile
+++ b/assays/Assay1/dataset/CPlantBox-isp/Doxyfile
--- a/assays/Assay1/dataset/CPlantBox-isp/LICENSE
+++ b/assays/Assay1/dataset/CPlantBox-isp/LICENSE
--- a/assays/Assay1/dataset/CPlantBox-isp/README.md
+++ b/assays/Assay1/dataset/CPlantBox-isp/README.md
+# CPlantBox
+[![DOI](https://zenodo.org/badge/95107851.svg)](https://zenodo.org/badge/latestdoi/95107851) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Plant-Root-Soil-Interactions-Modelling/CPlantBox/blob/isp/tutorial/jupyter/CPlantBox_PiafMunch_Tutorial_(include_installation).ipynb) [![Teaching Material LBRAI2219](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Plant-Root-Soil-Interactions-Modelling/CPlantBox/blob/isp/tutorial/jupyter/CPlantBox_Lesson.ipynb)\
+Two main functions
+1. Create plant structure
+2. Coupling with PiafMunch to have carbon and water flow inside the structure.
+
+# Create plant structure in 5 minutes
+
+The most convenient way is to use google colab, which is a Linux with jupyter notebook interface.
+You can click the link to follow the guide there, just to click some buttons and you will be able to create plants
+[here is the link to use it](https://colab.research.google.com/github/Plant-Root-Soil-Interactions-Modelling/CPlantBox/blob/master/tutorial/jupyter/CPlantBox_PiafMunch_Tutorial_(include_installation).ipynb)
+
+
+# Folder sructure
+
+/src			CPlantBox C++ codes
+/examples 		Some examples how to use the CplantBox
+/modelparameter		Some root parameter, and a plant parameter files
+/scripts 		Pyhthon scripts for visualization with Paraview, and Matlab scripts for parameter export
+/results 		Nice result images
+
+# Documentation
+
+Create the documentation by running doxygen in the folder 
+$ doxygen doxy_config
+
+The documentation should now be located in the folder /doc
+
+
+# Example
+
+# Examples
+Simulation videos availabe in Youtube Channel https://www.youtube.com/channel/UCPK-pFfpK94jiamgwHxX32Q
+
+[![Plant Simulations -- 8K resolution](https://media.giphy.com/media/LmBztw7mNwluJPJ3cU/giphy.gif)](https://www.youtube.com/watch?v=jNbvjW-WFvk "CPlantBox Simulations -- 8K resolution")
+
--- a/assays/Assay1/dataset/CPlantBox-isp/doxy_config
+++ b/assays/Assay1/dataset/CPlantBox-isp/doxy_config
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/2.sh
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/2.sh
+#!/bin/sh
+NAMESPACE=CPlantBox
+for x in $(find . -name "*.h"); do
+    sed -i "$(grep -n "^#" $x | tail -2 | head -1 | sed 's/:.*//')a\\\nnamespace $NAMESPACE {\n" $x
+    sed -i "$(($(grep -n "^#" $x | tail -1 | sed 's/:.*//')-1))a} // namespace $NAMESPACE\n" $x
+done
+
+for x in $(find . -name "*.cpp"); do
+    sed -i "$(grep -n "#include" $x | tail -1 | sed 's/:.*//')a\\\nnamespace $NAMESPACE {\n" $x
+    echo >> $x
+    echo "} // namespace $NAMESPACE" >> $x
+done
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/CMakeLists.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/CMakeLists.txt
+#
+# Make the C++ example
+#
+
+add_executable(test_cplantbox main.cpp)
+target_link_libraries(test_cplantbox CPlantBox)
+
+# link the model parameter folder (on Windows we have to copy since symlinks are not supported)
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    execute_process(COMMAND ${CMAKE_COMMAND} "-E" "copy" "${PROJECT_SOURCE_DIR}/modelparameter" "${CMAKE_CURRENT_BINARY_DIR}/modelparameter")
+else()
+    execute_process(COMMAND ${CMAKE_COMMAND} "-E" "create_symlink" "${PROJECT_SOURCE_DIR}/modelparameter" "${CMAKE_CURRENT_BINARY_DIR}/modelparameter")
+endif()
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/siltLoam.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/siltLoam.txt
+upperDepth,	lowerDepth,	Campbell_he,		Campbell_b,	VG_he,	VG_alpha, 	VG_n, 	VG_alpha_mod,	VG_n_mod, 		thetaR, 	thetaS, Ksat
+0.0, 		1.0, 		-2.08, 			4.74, 		-2.6,  	0.14, 		1.2, 	0.14,  			1.2,		0.05, 	0.43, 	0.003
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soil.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soil.txt
+upperDepth,	lowerDepth,	Campbell_he,	Campbell_b,	VG_he,	VG_alpha, 	VG_n, 	VGmod_alpha,	VGmod_n, 	thetaR, thetaS, Ksat
+0.0, 		0.2, 		-2.08, 			4.74, 		-2.6,  	0.14, 		1.2, 	0.2,  			1.2,		0.01, 	0.44, 	0.000167
+0.2, 		0.7, 		-5.15, 			2.59, 		-2.7,  	0.19, 		1.18, 	0.19,  			1.1,		0.01, 	0.45, 	0.000101
+0.7, 		1.0, 		-0.73, 			1.69, 		-0.7,  	0.68, 		1.7, 	0.68,  			1.7,		0.01, 	0.37, 	0.002814
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soilUniform.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soilUniform.txt
+upperDepth,	lowerDepth,	Campbell_he,	Campbell_b,	VG_he,	VG_alpha, 	VG_n, 	VGmod_alpha,	VGmod_n, 	thetaR, thetaS, Ksat
+0.0, 		1.0, 		-2.08, 			4.74, 		-2.6,  	0.14, 		1.2, 	0.2,  			1.2,		0.01, 	0.44, 	0.001
--- a/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soil_clay.txt
+++ b/assays/Assay1/dataset/CPlantBox-isp/examples/PSP_infiltrationRedistribution1D/soil_clay.txt
+upperDepth,	lowerDepth,	Campbell_he,	Campbell_b,	VG_he,	VG_alpha, 	VG_n, 	VG_alpha_mod,	VG_n_mod, 	thetaR, thetaS, Ksat
+0.0, 		1.0, 		-4.2, 			4.58, 		-3.8,  	0.15, 		1.35, 	0.3,  			1.33,		0.01, 	0.46, 	0.001
No results found