This project implements a self-avoiding walk for a three-dimensional polymer. The code include two part: create model and equilibrium (using LAMMPS).
To get started with this project, follow these few steps:
- Clone the repository: Clone this repository to your local machine using the following command:
git clone https://github.com/lp65082001/self-avoiding-walk-polymer.git
- Build environment Build the environment with docker:
docker build -f ./Dockerfile -t saw:v1 .
Run container (gpu version):
sudo docker run -i -t --gpus all -v /in this folder/:/root/ --name=saw_cuda saw:v1
Add environment parameter to pass mpi under root:
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
- Install LAMMPS Compile LAMMPS with gpu (option)
wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
unzip LAMMPS:
tar-xzvf lammps*.tar.gz
compile with gpu:
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create and use a build directory
cmake -D BUILD_MPI=yes -D LAMMPS_MACHINE=mpi -D PKG_GPU=on -D GPU_API=cuda -D GPU_ARCH=sm_86 -D PKG_OPT=yes -D PKG_PERI=yes -D PKG_KSPACE=yes -D PKG_MC=yes -D PKG_MOLECULE=yes -D PKG_RIGID=yes -D PKG_MPIIO=yes -D PKG_VORONOI=yes -D DOWNLOAD_PLUMED=yes -D PKG_USER-PLUMED=yes -D PKG_USER-OMP=yes ../cmake
cmake install:
cmake --build . # compilation (or type "make")
- How to use ? Using config.json:
{
"average_MW": 2800, # average molecular weight, unit: g/mol
"monomer_M": 28, # monomer molecular weight, unit: g/mol
"chains": 10, # number of chain
"bond_k": 18, # Bond spring, unit: kcal/mol/angstrom
"bond_l": 2.5, # Bond length, unit: angstrom
"angle_k": 2.06, # angle spring, unit: kcal/mol/radian
"angle_l": 168, # angle, # unit: theta
"epsilon": 0.25, # unit: kcal/mol
"sigma": 4.28, # unit angstrom
"num_sample": 1, # number of sample
"mode": "single_heter", # mode
"device": "cpu", # device
"model_init_save_path":"./model/" # save dir
}
- Implement method of Self-avoiding walk
- Create polymer model by using self avoiding walk
- Automate to using LAMMPS
- Automate create sample with random parameter
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