View plantfem.github.io on GitHub

(Latest update :: 14:12 2021-12-09)

Welcome to plantFEM

You can download the plantFEM to perform physical simulation for plants.

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Get started!

(1) Let’s download plantFEM into your local system:


git clone https://github.com/kazulagi/plantfem.git && cd plantfem && python3 install.py

(2) or you can run on Google Colab

!git clone https://github.com/kazulagi/plantfem.git 
%cd plantfem
!python3 install.py

(3) Also, docker is available

docker pull kazulagi/plantfem
docker run --rm -it kazulagi/plantfem /bin/bash

Then, let’s install plantFEM.


python3 install.py

When you install plantFEM, you’ll also get build and execution tools for Fortran since plantFEM is based on the modern Fortran. The plantFEM does lots of things:

  • search sample script plantfem search
  • create your new project with plantfem new
  • build & run your project with plantfem run
  • update your plantFEM plantfem update
  • check mannual with plantfem man
  • set hostfile for MPI with plantfem hostfile
  • change cpu-core for MPI with plantfem cpu-core

You can write a script on server.f90 in your root directory of plantFEM. If you want to use other modules written in Fortran, please set them into addon/ directory. All Fortran files in the directory is compiled with the plantFEM library before they are linked to your server.f90 script.

Further, you can easily use MPI by following steps.

  • set your hostfile at etc/hostfile
  • write number of cpu-cores in etc/cpucore or run plantfem cpu-core before running your script.

How to run your .f90 script?

Single process (Non-MPI):

plantfem build && ./server.out

With MPI:

plantfem build && mpirun -np $NUM_CORE ./server.out

Examples

Sample codes are available in Tutorial directory.

Scripts and coding

plantFEM consists of 4 components, each of which contains some libraries for numerical simulations. All examples runs when it is copied and pasted into server.f90 and executed by plantfem run command.

std

A standard library of Fortran prepared for plantFEM. This module extends fortran for easier use.

Try it from HERE » std

fem

A library for data-objects for FEM analysis.

Try it from HERE » fem

sim

A library for simulators for FEM analysis.

Try it from HERE » sim

obj

A library for realistic objects such as soybean, stem, leaf, soil, air, light …etc.

Try it from HERE » obj

Learn more