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

Specification

| plantFEM | | | ---- | ---- | | Developer | Haruka Tomobe & plantFEM.org | | Working state | current | | Written in | Fortran 2003, Python 3.x, C89 | |Source model | Open-source | | Initial release | 21.10 (20 October 2021)| | First Long-Term Surpport (LTS) release | 22.04 (23 April 2022) | | Repository | https://github.com/kazulagi/plantfem | | Usage | Agricultural CAE, Digital Twins for Agricultural/Civil Engineering |
| Target | Personal computers, HPC-Clusters, Servers | | Package Manager | soja (experimental) | |Platforms | x86-64 | |Default user interface | CLI | | Lisence | MIT | | Community | Slack (private channel) | | Official Website | plantFEM.org |

| Objects | Simulation | Simulation (experimental) | | ---- | ---- | ---- | | Elementary entities | Pseudo-static Deformation, Diffusion | Contact, Dynamic deformation, Reaction-diffusion | | Soybean | Creation, Measure size, Measure mass | Deformation, Contact, Photosynthesis | | Grape | Creation, Measure size, Measure mass | Deformation, Contact, Photosynthesis | | Maize | Creation, Measure size, Measure mass | Deformation, Contact, Photosynthesis |

| Library structure | | | ---- | ---- | | std | Extention of Fortran 2003. Contains fundamental classes for file-IOs and Mathematical operations.| | fem | Library for implementing Finite Element Method. You can create meshes (FEMDomain), shape-functions, boundary conditions, initial conditions and some elemental matrices.| | sim | A set of simulators for FEMDomain. Contains deformation, diffusion, and some experimental implementations. | | obj | A set of classes for realistic agricultural high-/low-level objects. High-level objects: Soil, Soybean, Maize, Grape...etc. Low-level objects: stem, leaf, air, light ...etc. |

| IO formats | | | ---- | ---- | | Input | json, vtk, msh, ASCII-text| | Output | json, vtk, msh, stl, ply, ASCII-text|

| Commands | | | ---- | ---- | | plantfem search | Search sample codes by a keyword | | plantfem install | Build library and setting PATH | | plantfem build | Build server.f90 and creates executable file server.out | | plantfem run | = plantfem build && mpirun ./server.out | | plantfem man | Manual for plantfem command. |

| Finite Elements | | | ---- | ---- | | 2-node line element | 1D 2D 3D| | 4-node isoparametric element | 2D| | 8-node isoparametric element | 3D|

| System Requirements | | | ---- | ---- | | Operation System | Linux (Ubuntu 16.04+, ElementaryOS, LinuxMint, Debian), Windows 10/11 (with WSL-Ubuntu), macOS | | CPU | 2 cores, 1.4 GHz| | RAM | 2 GB | | Storage | 1 GB |

| Dependancies (minimal) | version | | ---- | ---- | | git | 2.25.1 | | Python | 3.4 or later |

| Dependancies (Installed by setup/setup.py) | version, info | | ---- | ---- | | gcc | 6.4.0 or later | | gfortran | 4.8.0 or later (Fortran 2003 or later) | | mpif90 | = OpenMPI compiler, 2.x or later | | apt | 1.2.35 or later | | pip | pip3 or later | | curl | 7.47.0 or later |

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 .

1. 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

{.copy} 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.

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

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

plantfem load test.f90 plantfem build

1. Run your script.

./server.out

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

1. Execute

plantfem init

to initialize directory.

1. Edit server.f90

2. Build the project by

plantfem deploy

1. Run it by

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

Here is an example of hostfile

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

call plantfem from Python (experimental)

```python

import plantfem as pf

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

```Fortran module addonexample use plantfem type::addonexample_ ! Member variables real(real64),private :: realVal real(int32 ),private :: intVal contains ! methods (publicname => privatename) procedure :: set => setaddonsample procedure :: show => showaddonsample end type contains

! Definitions of methods

! ################################################ subroutine setaddonsample(obj,realVal, intVal) class(addonexample_),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 showaddonsample(obj) class(addonexample_),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 addonexample Compiling ./addon/addonexample.f90
addon_example.o | ########################### | (100%)

```

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

Fortran 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