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https://github.com/kazulagi/plantFEM

This is a plant/farming simulator based on Finite Element Method, which targets crops in fields and soil foundations. This software provides multi-physical simulations of agriculture for canopies, plants, and organs for farmers, breeders, agronomists, and civil engineers. Please try and give us feedback.
https://github.com/kazulagi/plantFEM

agriculture fem finite-element-methods

Last synced: about 2 months ago
JSON representation

Host: GitHub
URL: https://github.com/kazulagi/plantFEM
Owner: kazulagi
License: mit
Created: 2019-09-22T16:31:08.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2024-09-27T12:29:34.000Z (3 months ago)
Last Synced: 2024-10-29T22:31:36.829Z (2 months ago)
Topics: agriculture, fem, finite-element-methods
Language: Fortran
Homepage: https://github.com/kazulagi/plantFEM.git
Size: 304 MB
Stars: 42
Watchers: 4
Forks: 4
Open Issues: 6
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

open-sustainable-technology - plantFEM - A plant simulator based on Finite Element Method, which targets crops in fields. This software provides multi-physical simulations of agriculture for canopies, plants, and organs for farmers, breeders, and agronomists. (Consumption / Agriculture and Nutrition)

README

        ![Growth](https://user-images.githubusercontent.com/54159711/177001085-9ecd60a8-94b9-4848-b33e-af51545e1c9c.gif)

![soy_scalar_field](https://user-images.githubusercontent.com/54159711/147451703-cd0ecca3-5a87-4cc7-81e2-4621210dc0c4.jpeg)

![soyfield](https://user-images.githubusercontent.com/54159711/130534646-8bf5797a-f04f-4d05-aa47-6ca79a481a11.png)

![grass_leaf](https://user-images.githubusercontent.com/54159711/84125213-311c7480-aa77-11ea-8c61-e7bbce016f8a.gif)

![Civil_Engineering](https://user-images.githubusercontent.com/54159711/167798367-782058ff-e679-411d-a250-d3399e17fd21.png)

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

## Specification

| plantFEM | | 

| ---- | ---- | 

| Developer | [Haruka Tomobe](https://scholar.google.com/citations?user=aJsSCAYAAAAJ&hl=en) & [plantFEM.org](https://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](https://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).

[![Experimental](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1lPEzZnAS5CGuXjBw-P8VhMkcpoBxV4-k?usp=sharing)

# Documentation

## [Click here!](https://kazulagi.github.io/plantfem.github.io/)

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](https://plantfem.org/download/plantfem_22.04-ubuntu2004_amd64.deb)

## [[Click to download] Ubuntu 20.04](https://plantfem.org/download/plantfem_22.04-ubuntu2004_amd64.deb)

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.

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

```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="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

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1H5cmdKa9MJUC-22dHnvIgo8k6sdQ6NnF?usp=sharing)

Plant simulator based on Finite Element Method (FEM).

- Tutorial:

[Click here!](https://kazulagi.github.io/pf/)

## 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 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)

```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