Awesome

[New!] plantFEM 22.04(LTS) is released!

Specification

What's next plantFEM 22.10 ?

APIs for Python, C/C++, and JavaScript (Experimental).

Documentation

Click here!

For detail, you can create documentation by

ford ford.md

How to install

1. Clone the repository.

git clone https://github.com/kazulagi/plantFEM.git

2. Run python3 install.py. The default compiler is mpif90. If you want to use Intel compiler, run python3 install.py --compiler=intel instead of it.

For Windows users:

1. Activate your WSL2 (Windows 10)

2. Install "Ubuntu 20.04" from Microsoft Store

3. Run command

wget https://plantfem.org/download/plantfem_22.04-ubuntu2004_amd64.deb
sudo apt install plantfem_22.04-ubuntu2004_amd64.deb

1. You can open files by this command

explorer.exe .

5. Enjoy!

For Ubuntu users:

You can download pre-build packages for

[Click to download] Ubuntu 18.04

[Click to download] Ubuntu 20.04

In case you are using Ubuntu 18.04, execute the next one-liner.

wget https://plantfem.org/download/plantfem_22.04-ubuntu1804_amd64.deb && sudo apt install plantfem_22.04-ubuntu1804_amd64.deb

If you are using Ubuntu 20.04, execute the next one-liner.

wget https://plantfem.org/download/plantfem_22.04-ubuntu2004_amd64.deb && sudo apt install plantfem_22.04-ubuntu2004_amd64.deb

If you want to build and run as a docker container,

• (1) Activate "Docker for Windows" (https://docs.docker.com/docker-for-windows/)

• (2) Open command-prompt and run

git clone -b 22.04 https://github.com/kazulagi/plantFEM && cd plantFEM/docker

How to Use

1. Search sample codes

You can search sample codes by

plantfem search

and type your keywords.

2. Open editors (e.g. VSCode) and edit&save it with extention of .f90

3. Build your script (For example, test.f90) by

plantfem load test.f90
plantfem build

4. Run your script.

./server.out

Or you can run it with multi-core workstations or HPC-clusters.

1. Execute

plantfem init

to initialize directory.

2. Edit server.f90

3. Build the project by

plantfem deploy

4. Run it by

mpirun --hostfile [your hostfile for OpenMPI] -np [number of process] ./server.out 

Here is an example of hostfile

192.168.0.1  cpu=6
192.168.0.2  cpu=6
192.168.0.3  cpu=6

call plantfem from Python (experimental)

import plantfem as pf

soy = pf.soybean(name="hello_soy")
soy.create(config="./plantfem/Tutorial/obj/realSoybeanConfig.json")
soy.msh(name="hello_soy")
soy.json(name="hello_soy")

#soy.stl(name="hello_soy")

# path to plantfem
soy.run(path="./plantfem")

Try it now

Plant simulator based on Finite Element Method (FEM).

• Tutorial: Click here!

How to add modules for plantFEM?

(1) Create your Fortran add-on in plantfem/addon or other places. An example is shown in addon/addon_example.f90.

module addon_example
    use plantfem
    type::addon_example_
        ! Member variables
        real(real64),private :: realVal
        real(int32 ),private :: intVal
    contains
        ! methods (public_name => private_name)
        procedure :: set => setaddon_sample
        procedure :: show => showaddon_sample
    end type
contains

! Definitions of methods

! ################################################
subroutine setaddon_sample(obj,realVal, intVal)
    class(addon_example_),intent(inout) :: obj
    real(real64),optional,intent(in) :: realVal
    integer(int32),optional,intent(in) :: intVal

    obj%realVal = input(default=0.0d0, option=realVal)
    obj%intVal  = input(default=0, option=intVal)

end subroutine
! ################################################



! ################################################
subroutine showaddon_sample(obj)
    class(addon_example_),intent(in) :: obj
    print *, "Real-64bit value is :: ", obj%realVal
    print *, "int-32bit value is  :: ", obj%intVal
end subroutine
! ################################################

end module addon_example

(2) Compile your addon by typing "addon" after

plantfem

Then, type addon and tap ENTER

>>> addon
installing add-on
Directory path of your awesome addon is : (default path = addon)
> addon
installing from addon
addon_example
Compiling ./addon/addon_example.f90      
 >> addon_example.o
 | ########################### | (100%)
>>>

(3) Run your script (An example is shown in Tutorial/HowToUseAddon/ex1.f90)

program main
    use addon_example
    implicit none
    type(addon_example_) :: obj
    call obj%set(realVal=8.0d0, intVal=-100)
    call obj%show()
end program

(4) Done!

>>> test.f90
>
 Real-64bit value is ::    8.0000000000000000     
 int-32bit value is  ::   -100.000000    
>>> 

You can set a hostfile

vi ./etc/hostfile

and a number of process by

./plantfem cpu-core

or

vi ./etc/cpucore

logs;

• 2019/01/19 :: This Document is written.
• 2019/01/20 :: ControlParameterClass is included
• 2019/01/21 :: Bug Fixed :: FEMDomainClass/ExportFEMDomain.f90 about Neumann-Boundary
• 2019/01/21 :: "Method:DeallocateAll"::Deallocate all alleles.(For all objects)
• 2019/01/25 :: DisplayMesh.f90/ Implement >> Export Mesh data.
• 2019/02/19 :: DiffusionEquationClass.f90 >> Solver for diffusion equations with time-integration by Clank-Nicolson Method
• 2019/03/03 :: FiniteDeformationClass.f90 >> Solver for Finite Deformation problems (2D and 3D).
• 2019/03/10 :: FEMIfaceClass.f90 >> Interface objects (3D).
• 2019/03/10 :: MeshOperationClass.f90 >> Mesh can be devided and interface mesh ca be generated (3D).
• 2019/03/21 :: install.sh and run.sh is created.
• 2019/03/23 :: Standarize FEMDomain(.scf) objects
• 2019/03/24 :: Field class and Simulator Class are created.
• 2019/03/26 :: Interface Solvers are created as MultiPhysics
• 2019/04/13 :: PreprocessingClass is created.
• 2019/04/13 :: DictionaryClass is created.
• 2019/05/13 :: PreProcessingClass is created.
• 2019/06/29 :: ContactMechanicsClass is under debug
• 2019/08/01 :: Jupyter notebook is introduced as GUI.
• 2019/08/01 :: Installer for Windows/macOS/Linux is created.
• 2019/08/03 :: Delauney triangulation is now under development.
• 2019/09/06 :: Bugfix of Simulatior
• 2019/09/23 :: Source code is opened.Now solvers for diffusion, finite deformation, and diffusion-deformation coupling are available. Contact solver is under debugging.
• 2021/05/15 :: Now you can install plantFEM by install.py and can run by plantfem run
• 2021/10/21 :: Release plantFEM 21.10
• 2022/04/21 :: Beat-release: plantFEM 22.04

Acknowledgements

This project is financially supported by the following research grants.

• Grant-in-Aid for Young Scientists(Start-up), (ID:20K22599), JSPS, JAPAN
• Grant-in-Aid for JSPS Fellows, (ID:17J02383), JSPS, JAPAN

Relevant publications

[1] Haruka Tomobe, Kazunori Fujisawa, Akira Murakami, Experiments and FE-analysis of 2-D root-soil contact problems based on node-to-segment approach, Soils and Foundations, Volume 59, Issue 6, 2019, Pages 1860-1874.

[2] Haruka Tomobe, Kazunori Fujisawa, Akira Murakami, A Mohr-Coulomb-Vilar model for constitutive relationship in root-soil interface under changing suction, Soils and Foundations, Volume 61,2021, Pages 815–835.

[3] Haruka Tomobe, Yu Tanaka, Tomoya Watanabe, plantFEM: A Numerical Platform for Multi-physical Simulation of Plants, Third International Workshop on Machine Learning for Cyber-Agricultural Systems (MLCAS2021), Page 22.

[4] Haruka Tomobe, Vikas Sharma, Harusato Kimura, Hitoshi Morikawa, An Energy-based Overset Finite Element Method for Pseudo-static Structural Analysis. J. Sci. Comput. 2023, 94:55.

Others are under revision and/or under preparation.

TODO:

• Python-interface
• Spline curve
• NURBS curve