/Hmd

sample hoomd run

Primary LanguagePython

Instruction for installing hoomd

  1. Install Anaconda:
https://conda.io/projects/conda/en/latest/user-guide/install/linux.html

Python version 3.11 must be installed After Anaconda installing, change conda configuration setting to disable the automatic base activation:

conda config --set auto_activate_base false
  1. Create a conda virtual enviroment
conda create -n hmd python=3.11

where hmd is some name of the virtual enviroment

  1. Activate the created virtual enviroment:
conda activate hmd
  1. Install CUDA (if it is not installed and you use NVIDIA GPU):
sudo apt update
sudo apt install nvidia-cuda-toolkit
  1. Install hoomd for GPU:
export CONDA_OVERRIDE_CUDA="12.0"
conda install -c conda-forge "hoomd=4.2.1=*gpu*" "cuda-version=12.0"

or install hoomd for CPU:

conda install "hoomd=4.2.1=*cpu*"
  1. You should also install the GSD framework (https://gsd.readthedocs.io/en/stable/installation.html ):
conda install -c conda-forge gsd
  1. Also you can use nvtop, for example, to monitor a video card
sudo add-apt-repository ppa:flexiondotorg/nvtop
sudo apt install nvtop

nvtop

Ovito installing

https://www.ovito.org/linux-downloads/

Install the required system libraries using your Linux package manager:

On Ubuntu/Debian systems:

sudo apt-get install libxcb1 libx11-xcb1 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
            libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 \
            libxcb-sync1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb-cursor0 \
            libfontconfig1 libfreetype6 libopengl0 libglx0 libx11-6