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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).

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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!

<!--   [使い方：日本語版 >> ](https://qiita.com/soybean) https://qiita.com/soybean [ <std #1> Standard math library for plantFEM >> ](Tutorial/playon_std/ex0001_math.f90) [ <std #2> Kernel for file-IO >> ](Tutorial/playon_std/ex0002_fileIO.f90) [ <std #3> Standard array-operation library for plantFEM >> ](Tutorial/playon_std/ex0003_array.f90) [ <std #4> Linear solvers for plantFEM >> ](Tutorial/playon_std/ex0004_linearsolvers.f90) [ <std #5> Kernel for parallel computing using MPI >> ](Tutorial/playon_std/ex0005_mpi.f90) ## New! sample codes and tutorials of module "fem" [ <fem #1> domain-creation library for plantFEM >> ](Tutorial/playon_fem/ex0001_mesh.f90) ## How to use plantFEM as a blender-addon. [How to use plantFEM as a blender-addon. >>](doc/BlenderAddon.md) <!-- ## How to run your *.f90 script with plantFEM. ### Command-line mode: ``` plantfem your_script.f90 ``` ### Interactive mode ``` python3 plantfem.py >>> your_script.f90 ``` ## Environment ### Google Colab !new! This can run in Google-Colab. Installation: ``` !git clone -b 21.10 https://github.com/kazulagi/plantfem.git %cd plantfem %ls !python3 install.py !plantfem install ``` Execution: ``` !./plantfem your_script.f90 ``` ### Linux #### Ubuntu 18.04 ``` sudo apt update sudo apt upgrade -y sudo apt install git git clone -b 21.10 https://gitlab.com/kazulagi/plantfem.git cd plantfem sudo apt install python3 python3 setup/setup.py jupyter-notebook ``` - Execute Gmsh and go to Tools>Mesh>General and check "Recombine all triangular meshes", then, click File>Save Option As Default and close window. ### macOS (Mojave) Install homebrew (https://brew.sh/index) ``` /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" ``` And, install other applications. ``` brew install git git clone -b 21.10 https://gitlab.com/kazulagi/plantfem.git cd plantfem brew install python3 python3 setup/setup.py jupyter-notebook ``` ### Windows (10.0) Please activate Windows Subsystem for Linux (WSL) and install Ubuntu 18.04 according to the article. (Windows